Make a career path with us

“The strength of the team is each individual member. The strength of each member is the team.” – Phil Jackson

Our Values

Icon of warrior bow
Warrior Spirit
Sound Judgement
five hands together
All for One


In addition to a stimulating and rewarding workplace, Annexon offers a competitive base salary and equity participation, as well as a comprehensive health benefit package, which includes medical, dental, vision, 401(k) and flexible spending plans. We are located in South San Francisco, CA with shuttle service from BART, CalTrain and the Ferry.

Open Positions

We are looking for talented individuals to join our experienced, collaborative and driven team. Those who are passionate about making a difference in the lives of patients and their families and who bring that drive and dedication to the workplace are encouraged to apply to our open positions below.

Associate Director/Director CMC


This position reports into the Vice President of CMC & Supply Chain Logistics. The Associate Director or Director will oversee efforts to develop and manufacture drug substance and drug product and to track clinical drug inventory.


· Act as a supporting contact to oversee production activities at CMOs and provide technical support and troubleshooting.

· Collaborate with other functions at Annexon to develop and implement specifications for drug substance and drug product specifications and if needed, collaborate with QA and other functions to manage out of specifications, deviations and investigations.

· Collaborate with Clinical Operations to ensure that drug supplies are available on-time for support of clinical studies.

· Author and/or review batch records, change controls, and other technical documents.

· Oversee the development and validation of analytical methods according to ICH guidelines to ensure effective characterization and release of clinical batches.

· Design and oversee formulation development and stability studies for drug substance and drug product for multiple compounds.

· Collaborate with QA, Regulatory Affairs and other functions towards timely generation of regulatory documents.

· Work with discovery project leaders to determine if a viable initial development pathway for initial development exists for molecules being considered as development candidates.

Qualifications and Other Required Knowledge and Skills:

· A BS/MS/PhD in Analytical Chemistry, Biochemistry, or Pharmaceutical Chemistry is required, with 10+ years of related industry experience in drug substance and/or drug product development, production and analysis.

· An in-depth knowledge and drug development experience in biologics, preferably monoclonal antibodies,is strongly desired, from early to BLA stage development.

· Familiarity with protein purification, protein analytical and characterization techniques.

· Familiarity and working knowledge of GMP/ICH regulations required, with experience working in a GMP facility preferred.

· Team oriented professional with excellent organizational, communication, leadership and problem-solving abilities.

· Working knowledge of quality by design and risk management is strongly desired. Knowledge of ICH Q8/Q9 and Q10 is preferred.

· Experience overseeing external CRO based resources for production of drug substance and drug product.

· Demonstrated ability to successfully coordinate multiple work streams and development efforts in a timely and economically responsible manner in small, start-up biotech companies.

· Experience and familiarity with successful operation in the biologics CMC regulatory environment for early to mid-stage development.

Apply Online

Associate Director/Director, Program & Portfolio Management


Associate Director/Director, Program & Portfolio Management

Position Overview

The Associate Director/Director, Program & Portfolio Management is a proactive and effective problem solver who is intellectually curious and works exceedingly well with others. This role is responsible for managing and driving cross-functional activities required to advance a program from preclinical development through BLA submission. The winning skill set includes working effectively and efficiently with cross- functional groups including nonclinical, clinical, technical development, regulatory, manufacturing, commercial planning and finance. As a key member of the Core Team, the Associate Director/Director, Program & Portfolio Management will work closely with the GPL (Global Program Leader) to help establish and execute program strategy and activities, integrate cross-functional input, synthesize team recommendations, and ensure program advancement on time and on budget. Lastly, the Associate Director/Director, Program & Portfolio Management is expected to create and maintain consistent project documentation including project plans, timelines, trackers and communications.

Specific Responsibilities

· In partnership with GPL and Core Team, develops and maintains integrated product development and lifecycle plans.

· Creates and maintains project timelines that are critical tools for tracking progress against goals; closely and transparently manages the critical path of the project.

· Proactively identifies critical milestones, interdependencies, risks and resource constraints that could impact project timelines and collaborates with teams to develop appropriate solutions.

· Co-facilitates Core Team Meetings with GPL.

· Responsible for Core Team documentation including meeting agendas, minutes, action item and decision trackers.

· Ensures that all team members are fully informed and knowledgeable of project activities and status; optimizes communication within and between teams, in and outside of meetings.

· Partners with Core Team to proactively address acute issues that arise.

· Ensures that consistent project management tools and practices are used across team.

· Supports continuous improvement efforts in Project Management practices at Annexon; leads department initiatives.

· Ensures compliance with corporate policies and procedures, as well as, US healthcare laws and regulations.

Position Qualifications

· Undergraduate degree in a scientific, medical or business discipline; postgraduate qualification (e.g., Ph.D., MBA, MS) or commensurate experience is a distinct advantage.

· A minimum of 8 years of biopharmaceutical industry experience, with half in a Project Management function supporting highly matrixed drug development teams comprised of, but not limited to, functional area representatives from Research, CMC, Regulatory, Clinical, Marketing and Finance.

· Solid understanding of activities critical to early and late stage drug development projects; commercial-stage a plus.

· Proven ability to manage complex, cross-functional development projects with Go/No Go decisions.

· Well-versed at scenario planning and capable of rapidly integrating new information into existing plans.

· Excellent meeting planning and facilitation skills.

· Highly proficient at both building and maintaining Gantt charts, tracking systems, spreadsheets and tools that support a systematic and scalable approach to managing projects.

· Highly organized, excellent writing and oral communication skills, motivated and analytically rigorous.

· Experienced at partnering with team members to determine planning assumptions that drive timelines and budgets.

· Adept at skillfully managing complex and challenging situations.

· Team-oriented, with excellent interpersonal skills (i.e. collaboration, conflict management and negotiation).

Apply Online

Clinical Trial Manager/Senior Clinical Trial Manager


The CTM/Sr. CTM is responsible for the operational management, oversight and execution of one or more clinical trials including CROs, vendors, and consultants as needed for the conduct of clinical studies.  This individual will report to the Sr Director, Global Clinical Operations. 


  • Provides full management of 1 or more studies within the Annexon portfolio of clinical trials
  • Provides study leadership and effectively collaborates with other departments and functional groups to meet study timelines and corporate goals
  • Independently creates and/or oversees the design of study related documents including but not limited to: clinical protocols, case report forms, study manuals and plans, informed consent forms, safety committee charters 
  • Manages study-specific CROs, vendors and contractors
  • Reviews CRO and vendor scope of work / work orders
  • Works closely with CROs to set up study systems, such as safety management, data management, clinical monitoring, TMF, etc.
  • Responsible for review and approval of IP release packages
  • Management of the labeling and distribution requirements of the IP
  • Works together with the Senior Director to develop and track study budgets and financial forecasting
  • Prepares study updates and tracking information for departmental / company meetings
  • Establishes and leads study management team meetings internally at Annexon and via teleconferences with study vendors
  • Prepares and presents study-specific slide presentations during Investigator Meetings. Leads training sessions for the training of CROs and field CRA’s
  • Attends scientific meetings as a representative of Annexon clinical operations team
  • Proactively identifies and communicates study-related issues and facilitates discussion of potential solutions that can be implemented by the team
  • Exercises professional judgment in selecting methods and techniques for obtaining optimal results
  • May participate in clinical research SOP development or updates as appropriate
  • Uses well-developed problem-solving skills to address needs of program and provides leadership and guidance to others
  • Attends site initiation visits, as applicable, as a representative of the study sponsor


  • BA / BS, RN or higher degree
  • 5+ years (CTM) or 8+ years (Sr. CTM) clinical operations experience, in the pharmaceutical / biotech industry
  • Experience with managing CTMs, CRAs and Clinical Assistants
  • Experience with early phase trials, ophthalmology, immunology, and neurology is beneficial
  • Experience working within a small biotech company preferred
  • Working knowledge of GCP/ICH guidelines and the clinical development process
  • Management of international clinical studies  
  • Experience managing CROs, lab vendors and other support vendors
  • Knowledge of data management process, including database build activities
  • Proficient with MS Word, Excel and PowerPoint
  • Strong interpersonal, communication (written and verbal), and organizational skills
  • Ability to work independently as well as part of a multi-functional study team, with a willingness to take on tasks outside of the typical job responsibilities
  • Available for travel domestically and internationally (approx. 5-20%, depending on study phase) 
Apply Online

Director, Financial Planning & Analysis

General & Administrative

Company Summary

Annexon Biosciences is a clinical-stage biopharmaceutical company developing a pipeline of novel therapies for patients with classical complement-mediated disorders of the body, eye and brain. The Company’s pipeline is based on its platform technology addressing well-researched classical complement-mediated autoimmune and neurodegenerative disease processes, both of which are triggered by aberrant activation of C1q, the initiating molecule of the classical complement pathway. The Company’s first product candidate, ANX005, is a full-length monoclonal antibody formulated for intravenous administration in autoimmune and neurodegenerative disorders. The Company’s second product candidate, ANX007, is a monoclonal antibody antigen-binding fragment (Fab) formulated for intravitreal administration for the treatment of neurodegenerative ophthalmic disorders. Based on learnings from its initial trials, Annexon is advancing its current programs while evaluating additional orphan and large market indications. Annexon is deploying a disciplined, biomarker-driven development strategy designed to establish that each of its product candidates is engaging the specific target at a well-tolerated therapeutic dose in the intended patient tissue.

Desired Candidate Profile

The FP&A Director is a high impact, executive-facing role that will report directly to the VP, Controller, and support Annexon’s critical pipeline milestones, as well as the company’s growth toward becoming a multi-product commercial-stage biopharmaceutical company. The FP&A Director will have a key role in supporting multiple functional areas and project teams within the Annexon organization. The role will have the unique opportunity to build and work on budgets for various stages within the clinical development process across the Annexon portfolio.  This role will partner closely with leaders across clinical operations, manufacturing, and project management to drive the annual budget process, regular forecasts as well as the long- range plan.  Success in this role will require cultivating partnerships across teams, strong communication, ability to influence, and strategic thinking skills to drive value to the business.

Specific Responsibilities

  • Partner with stakeholders to coordinate and develop annual budget and periodic forecasts, including OPEX, capital spend and headcount.
  • Work with project management organization to leverage external data to understand and challenge expense projections for short- and long-term financial models.
  • Work closely with department heads to review complex clinical and manufacturing contracts for costs and payment terms during the contract negotiation.
  • Collaborate with cross-functional leaders to create monthly reporting dashboard to track key financial and performance metrics.
  •  Perform budget versus actual analysis at the consolidated, project, and department levels to identify and understand variances, assess associated risks and opportunities, and communicate results to senior management.
  • Perform assessment FP&A system requirements and near-term implementation to support needs of the organization.
  • Support adhoc requests as needed. Provide financial assessments and guidance for strategic projects and business cases.
  •  Develop and deliver presentations to senior management with clear and concise objectives, analyses, and recommendations.

Key Qualifications:

  • Bachelor’s degree in finance or accounting required.
  •  CPA and/or MBA preferred.
  •  Minimum of 8-10 years of increasing responsibility in finance or accounting.
  •  Professional experience in a biotechnology, pharmaceutical, or medical device organization.
  • Prefer experience in company with late stage development or commercial stage products.
  •  Ability to establish strong business relationships and interact cross-functionally at all levels.
  • Must possess strong problem-solving skills. Ability to work effectively to identify issues, gather relevant data points and recommend solutions.
  • Must be a strong communicator capable of explaining/presenting complex financial concepts and problems clearly and effectively to all constituents.
  •  Customer service oriented; able to understand business requirements while maintaining ownership for projects and results.
  • Highly detail oriented with strong analytical skills; experienced in developing financial models, leading analysis, and explaining options and implications.
  • Highly motivated self-starter capable of working under pressure and prioritizing workload to meet deadlines.
  •  Strong team player with ability to demonstrate executive presence.
  • Process and systems improvement mindset for creating solutions to problems that work across boundaries beyond this role
Apply Online

Head of Clinical Biomarkers


Head of Clinical Biomarkers 

The Head of Clinical Biomarkers is responsible for developing and implementing strategies for clinical biomarkers across the entire Annexon discovery and development portfolio. This strategy is critical to Annexon’s precision medicine approach in the key therapeutic areas of Autoimmune diseases, Neuroscience and Ophthalmology. This individual will serve as an important Annexon leader and integrator between research and development. He/she will also oversee operational aspects such as the collection and analysis of all clinical biosamples and interfacing with external vendors to obtain timely and high-quality data.


• Develop biomarker strategies to enable precision medicine approaches and optimal selection of patient indication and patient subsets in clinical trials.

• Develop biomarker strategy to align the clinical development plan from Phase I to III.

• Supervise biomarker assay development, validation and implementation.

• Lead operations for collection, management and analysis of clinical trial patient biomarker samples.

• Develop biomarker analysis plan and oversee biomarker data analysis; leads the analysis of biomarkers for clinical studies by working with key internal stakeholders and external CROs as needed.

• Provide consultation to pre-clinical programs to drive formulation of biomarker strategy at an early stage of development.

• Responsible for the integration of scientific learnings and clinical biomarker data to define targeted patient populations and enable selection of potential diagnostic platforms.

• Provides expert guidance to multi-disciplinary teams and senior management; act as the Biomarker representative on Project teams.

• Author biomarker strategy documents, biomarker specific portion of clinical protocols, and regulatory documents.

• Use biomarkers to identify opportunities to study compounds in new indications/combinations. • Identify, establish and oversee external collaborations with key opinion leaders, academic sites, and CROs to advance our understanding of disease pathways and prognostic/predictive biomarkers.

Key Qualifications:

• PhD and/or post-doc training in the area of immunology, or other related medical science field with a minimum of 15 years of relevant biotechnology or pharmaceutical industry experience.

• Knowledge of biomarker discovery and development, assay development/validation, clinical discovery of biomarkers, and MoA/translational research.

• Candidate must be detail-oriented with excellent record keeping and organizational skills.

• Must be a highly flexible, results oriented, independent self-starter who enjoys working in a fast-paced and dynamic, team-oriented environment.

• Excellent collaboration, communication, and interpersonal skills are required to engage and be productive within a high achieving team environment.

• Ability to integrate complex scientific ideas, generate testable hypotheses, and execute broad understanding of drug discovery and development in both early and late stage development.

• Familiarity with regulatory approval process.

• Basic understanding of technical aspects of companion diagnostics development

• Proven scientific/leadership expertise (working in teams, managing people/projects commensurate with a senior level).

• Strong experimental background and experience in hypothesis-driven biological/translational research with demonstrated ability to execute well-designed experiments.

Apply Online

VP, Medical Affairs


Reporting into the Chief Medical Officer, the Vice President, Medical Affairs will be a core member of the clinical and medical team and will establish and lead the Medical Affairs function at Annexon Biosciences. The Vice President, Medical Affairs will be responsible for driving Annexon’s growth by providing strategic and operational leadership both cross-functionally and to a team that they will build from the ground up. This role will ultimately be responsible for ensuring launch readiness for multiple assets across multiple therapeutic areas.


  • Establish and lead the Medical Affairs function at Annexon Biosciences.
  • Oversee medical communications, medical education, congresses/conferences, KOL outreach and advisory boards; convey role of Annexon’s lead compounds in treating autoimmune and neurodegenerative diseases.
  • Work closely with cross-functional partners to understand current medical practice in the diseases of interest and what is needed to address the unmet needs from the clinical and health economics perspective. 
  • Develop and implement key medical affairs strategies and activities to support the late stage development of Annexon’s lead assets.
  • Represent company externally, oversee medical affairs aspects of development and pre-launch needs. 
  • In collaboration with the Senior leadership develop medical affairs vision, mission and department plan in alignment with related functions that will interface with the department.
  • Provide external facing leadership with KOLs. 
  • Contribute to company success through both internal and external medical education and medical/scientific information exchange and support.
  • Build relationships with key opinion leaders by providing disease state education and communicating the clinical value of Annexon’s scientific platform.


  • MD with 15+ years’ experience, including at least five years of previous biopharmaceutical industry experience 
  • Experience with prelaunch and diseases in autoimmune and neurodegeneration desired
  • Ability to understand and effectively communicate scientific and medical information to both internal and external networks, in support of the scientific and business strategy 
  • Demonstrated leadership skills and experience building effective teams 
  • Excellent written and oral communication skills 
  • Ability to anticipate and adapt to change 
  • Strong interpersonal skills commensurate with the need to work closely with partners, KOL’s, consultants, and team members across functions 
  • Ability to communicate well with health care professionals; ability to establish strong relationships with peer groups, professional organizations, and other outside parties 
  • Ability to travel up to 20% 
Apply Online

VP, Ophthalmology


Reporting into the Chief Medical Officer, the Vice President, Ophthalmology Development will be responsible for driving Annexon’s growth by providing strategic and operational leadership both cross-functionally and to a team that They will build from the ground up. This role will entail the development, implementation, and oversight of a robust early development process for Ophthalmology-focused scientific initiatives within the company.

The Vice President will be a core member of the clinical and medical team and will contribute to devising the overall clinical strategy and ensure all activities occur in compliance with the appropriate regulations. They will provide support to translational medicine efforts within Ophthalmology, working closely with research and preclinical development to define strategy and transition compounds from research into development candidates, and ensure their effective, timely de-risking while ensuring time- and cost-efficiency of the clinical development plan and clinical trial design.


  • Lead the design and execution of clinical trials for ophthalmology focused diseases in collaboration with cross-functional partners
  • Collaborate across all levels in the organization, including effective cross-functional interactions with R&D, program leadership, etc.
  • Formulate clinical development plans (CDP) that integrate scientific rationale, clinical need, clinical measurement approaches, statistical rigor, regulatory and payor requirements, and company strategy
  • Develop and implement high quality clinical studies to support the CDP including biomarker and translational studies
  • Provide medical monitoring, safety assessment, and overall oversight for all clinical trials within Ophthalmology
  • Serve as a content expert in the review of abstracts, publications, medical information letters, and other medical documents as needed
  • Provide medical input into regulatory document preparation
  • Lead content development for advisory board meetings
  • Contribute to company success through both internal and external medical education and medical/scientific information exchange and support
  • Build relationships with key external stakeholders including, but not limited to healthcare professionals at key institutions, patient advocacy groups, and regulators by providing disease state education and communicating the clinical value of Annexon’s scientific platform
  • Drive a high-performance culture by fostering innovation, personal accountability, and commitment for results


  • Ophthalmologist MD with 15+ years’ experience, including at least five years of previous biopharmaceutical industry experience 
  • Expertise and awareness of the landscape in early stage development in the Ophthalmology space 
  • Proven expertise in translational medicine and biomarker development 
  • Experience executing and analyzing proof-of-concept studies to drive programs forward strongly preferred 
  • Understanding of adverse events and safety packages preferred 
  • Ability to understand and effectively communicate scientific and medical information to both internal and external networks, in support of the scientific and business strategy 
  • Demonstrated leadership skills and experience building effective teams 
  • Excellent written and oral communication skills 
  • Ability to anticipate and adapt to change 
  • Strong interpersonal skills commensurate with the need to work closely with partners, investigators, contractors, consultants, and team members across functions 
  • Ability to communicate well with health care professionals; ability to establish strong relationships with peer groups, professional organizations, and other outside parties 
  • Ability to travel up to 20% 

Apply Online

VP, Project Team Leader


Company Overview:

Annexon Biosciences is a clinical stage biotechnology company focused on developing novel inhibitors that are designed to block C1q and the entire classical complement pathway. We are pioneers in targeting C1q, the initiating molecule of the classical complement pathway. By stopping the start of this pathway, our C1q inhibitors are designed to treat multiple complement-mediated autoimmune, neurological and ophthalmic diseases of the body, brain and eye. Annexon is headquartered in South San Francisco CA.

As the leader of one of our therapeutic franchises, the VP, Project Team Leader will provide strategic scientific, business and operational leadership and direction of the R&D development and advancement of Annexon’s portfolio. In addition to developing and driving a comprehensive lifecycle portfolio strategy, the VP, Project Team Leader shall be responsible for leading a cross functional leadership team of both internal and external resources in all aspects of development pre-IND stage through late stage development, ensuring consistent high quality output from the team and achievement of program goals and objectives as well as drive effective execution of such strategies by leading the cross functional team’s engagement, integration, coordination and communication across functional lines. Duties for this role also include managing R&D partnerships, helping to build necessary infrastructure for the R&D organization and working with the executive leadership to create an environment that supports rapid and high quality decision making (both for the portfolio and the organization) and to identify, evaluate and find solutions for key issues facing the programs on an ongoing basis.

Key Responsibilities:

  • Partnering with internal and external stakeholders to drive the development of a comprehensive strategic plan through registration and pre-commercialization preparation, including goals, budget and risk assessment. Includes developing program vision, strategy, scope/focus, milestones, risk assessment and management strategies, as well as project investment requirements.
  • Leading cross-functional Project Team focused on the development of Annexon’s clinical candidates, from pre-IND through late stage clinical development and NDA submission for multiple indications. Project Team shall include representation from Research, Development, CMC, Regulatory, Quality, Commercial and Finance.
  • Providing effective leadership and direction to the cross functional Project Team, including scientific and operational oversight of activities, budgeting and planning.
  • Utilizing his/her understanding of disease biology, global drug development and portfolio management within the field of Neuroscience and/or Autoimmune disorders to effectively lead the Project Team.
  • Partnering with executive team to develop operating framework within R&D, including with regard to the Project Team to clarify and facilitate decision-making and escalation around strategic direction, resource allocation, etc.
  • Partnering with functional areas to identify and ensure adequate resources for timely completion of goals and objectives. Ensuring team members understand program objectives, specifications, deliverables, timelines, and tasks.
  • Driving the development and implementation of lifecycle portfolio strategy and follow- on drug candidates for multiple diseases.
  • Managing and communicating program progress on a continual basis, identifying both cross-program and cross-functional issues, resource issues, timeline issues, and budget issues.
  • Works on significant and unique issues where analysis of situations or data requires an evaluation of intangibles
  • Exercises independent judgment in methods, techniques and evaluation of criteria for obtaining results
  • Participates in corporate development of methods, techniques and evaluation criteria for projects, programs and people
  • Ensures budgets and schedules meet corporate requirements
  • Creates formal networks involving coordination among groups. Regularly interacts with executives and/or major internal and external customers
  • Works on abstract problems across functional areas of the business.
  • Identifies and evaluates fundamental issues for major function areas through assessment of intangible variables. In-depth knowledge of functional areas, business strategies and company goals.
  • Interacts internally and externally with executive level management requiring negotiation of matters to influence policy making bodies both internally and externally.
  • Anticipates potential roadblocks and issues of conflict and maintains open lines of communication in problem solving and resolving issues and conflict.


  • Leadership: Experience leading and motivating teams in a matrix environment is required. Proven interpersonal skills with ability to influence, resolve conflict and drive decisions among internal cross functional teams, executive management, and external teams.
  • Strategic Agility: Ability to develop and execute complex strategies.
  • Collaboration/Relationship Management: Ability to effectively collaborate in and across multiple functions, and with internal and external stakeholders of various backgrounds and skill sets. Skilled in establishing a collaborative and respectful environment.
  • Influencing: demonstrated skills in persuading senior leadership on strategy, initiative(s) implementation, and decision-making. Influences and motivates others to achieve objectives.
  • Decision Making: Strong decision-making skills taking multiple perspectives into account and analytical skills are required; exercises sound business judgment that has broad organizational impact.
  • Communication: Excellent communication skills (both orally and written) is critical to the success of the role.
  • Business Excellence: good at developing the processes necessary to get things done,knows how to organize people and activities and knows what to measure and how to measure. Demonstrated ability to interpret data into actionable items.
  • Negotiation: Proven negotiation skills that effectively drive discussions and decisions to desired end-results that have broad organizational impact.


  • The successful candidate should have an advanced degree in life sciences or medicine (MD or PhD) and or an MBA. He/she will have at least 10 years of industry experience in drug development, including experience in early phase non-clinical and clinical drug development, regulatory knowledge and pre-commercial market preparation.
  • Prefer scientific or industry experience within the autoimmune, neurology and/or ophthalmology field.
  • Will have a proven track record of being a results-oriented leader and will have 5+ yrs. leading, managing, and developing program related teams.

Apply Online

Annexon is an equal opportunity employer & prohibits unlawful discrimination based on race, color, religion, gender, sexual orientation, gender identity/expression, national origin/ancestry, age, disability, marital & veteran status.