Associate Director Program Manager - Gene Therapy Career

Encoded Therapeutics; South San Francisco (CA); On-site; USD 170,000 - 205,000; Full time

Benefits offered by this job

Comprehensive benefits package

PTO, sick time and holiday pay

Generous Parental Leave

Pre-tax medical and dependent care

STD, LTD, Life and AD&D

Team-building events

Fully stocked micro-kitchen

Fitness center at South San Francisco

Job summary

Encoded Therapeutics is seeking an Associate Director, Development Program Manager to drive cross-functional planning for an AAV gene therapy CNS program. You will partner with Research, Clinical Development, Regulatory Affairs, CMC, Medical Affairs, and Patient Advocacy to ensure timelines, budgets, risks, and deliverables stay on track.

The role reports to the Director, Development Program Management. The ideal candidate brings 8+ years in biotech/pharma program management and experience with

Qualifications

• Minimum 8 years related experience with bachelor's; 6 years with master's; 3 years with PhD; equivalent experience.
• Advanced degree in life sciences/pharmacology; MBA or PMP a plus.
• Experience in program/project management within biotech/pharma.

Responsibilities

• Facilitate development and implementation of program strategy, aligning with timelines and budgets.
• Organize cross-functional Development Core Team activities for collaboration and milestone alignment.
• Track deliverables and manage risks across Research, Nonclinical, Clinical, Regulatory, CMC, Medical, and Patient Advocacy domains.
• Support budgeting, resource planning, and dashboard/reporting to leadership.

Job description

Associate Director Program Manager - Gene Therapy Career — Remote

This Associate Director role at Encoded Therapeutics represents a strong mid-to-senior career move for biotech program managers with 6–10+ years of experience in life sciences. Here's what makes it notable:

Compensation & Market Position: At $170,000–$205,000 (Bay Area) or $160,000–$189,000 (elsewhere), this is competitive but not exceptional for an Associate Director-level PM role at a clinical-stage biotech. Industry benchmarks typically place AD-level program managers at $160,000–$220,000 in the Bay Area, with the upper end reserved for therapeutic leads or dual scientific/PM expertise. The addition of stock options in a pre-commercial gene therapy company adds meaningful upside potential.

Skills You'll Build:

• Deep expertise in AAV gene therapy program management — one of the most specialized and in-demand skill sets in biopharma
• CNS rare disease drug development, an area with growing pipeline investment industry-wide
• AI-assisted PMO tooling and workflow modernization — a differentiating skill for future senior PM roles
• Cross-functional leadership and executive stakeholder communication (BoD, QBR)

Culture & Growth Signals: Encoded is a focused, mission-driven biotech (not a mega-pharma), suggesting a lean team where individual impact is high. The PMO appears to be maturing, which is a green flag for someone who wants to shape processes, not just follow them.

Potential Red Flag: The 20% travel requirement and fast-paced environment signal high workload. Candidates should clarify work-life balance expectations and team staffing levels before accepting.

Encoded Therapeutics Inc. is a biotechnology company advancing precision medicines for a broad range of genetic disorders. Our mission is to unlock new opportunities for viral gene therapy through genomics-driven discovery. We focus on delivering life-changing advances for individuals with genetic disorders not addressable with current approaches. For more information, please visit www.Encoded.com .

Encoded is seeking an Associate Director, Development Program Manager to drive the cross-functional planning and execution of a development program within our AAV gene therapy platform, focused on central nervous system (CNS) indications. Reporting to the Director, Development Program Management, this role is for an experienced program management professional who combines strong organizational and project-management expertise with a solid understanding of the drug development process, ideally including gene therapy or other advanced modalities. The Associate Director will serve as the operational backbone for the program team, working closely with Research, Clinical Development, Regulatory Affairs, CMC, Patient Advocacy and Medical Affairs to ensure program timelines, budgets, risks, and deliverables stay aligned and on track, while partnering with and escalating to the Program Management Organization (PMO) Director on major risks, resourcing conflicts, and strategic trade-offs.

Responsibilities

Program Strategy & Core Team Leadership

• Facilitate development and implementation of program strategy, ensuring alignment with company goals, timelines, and budgetary constraints
• Organize Development Core Team activities that foster cross-functional collaboration, effective communication, and strategic discussion, ensuring all stakeholders are aligned on program objectives and milestones to aid decision-making
• Ensure cross-functional teams are properly prepared for internal meetings, communications to management, and engagement with external partners
• Partner with the Director of PMO to ensure portfolio and cross-program considerations alignment

Program Planning & Execution

• Develop and maintain the integrated program plan, timeline, and budget across all functional areas (Research, Nonclinical, Clinical, Regulatory, CMC, Medical, Patient Advocacy, Commercial) for the assigned program
• Track deliverables resulting from Core Team meetings, ensuring timelines are met and objectives are achieved
• Identify program risks and dependencies early, and develop and track mitigation plans in partnership with functional leads, with particular attention to the specialized considerations of AAV gene therapy programs (e.g., viral vector supply timelines, long-term follow-up requirements, specialized dosing or delivery infrastructure for CNS administration)
• Assist functional leads with implementing risk management strategies, proactively identifying and mitigating program risks and challenges
• Support scenario planning and contingency planning for key program decision points (e.g., go/no-go milestones, regulatory interactions, data readouts)
• Contribute to the development and refinement of program management processes, templates, and best practices across the organization

Cross-Functional Coordination

• Serve as the primary point of integration across functional areas for the program, ensuring consistent communication of program status, risks, and decisions
• Partner with functional leads to coordinate cross-functional projects related to CMC, Regulatory, Clinical, Medical, Patient Advocacy, and Nonclinical, providing support and guidance to achieve project goals
• Facilitate internal communication to identify risks and mitigations, escalating unresolved issues to the Director PM as needed

Budget & Resource Management

• Partner with Finance and functional leads on budget forecasting
• Support resource planning and capacity analysis across functions to ensure the program is appropriately staffed

Communication & Reporting

• Monitor and report program progress, providing regular updates to cross-functional teams, the PM Director, and other stakeholders, highlighting key achievements, challenges, and mitigation plans
• Utilize formal communication protocols and tools, including dashboards, reports, and weekly/monthly updates, to support company and operational goals
• Support maintenance of program documentation in alignment with internal quality and compliance standards

Ad Hoc Projects

• Demonstrate flexibility and adaptability to contribute to ad hoc functional projects across various departments
• Collaborate with team members to address challenges and find innovative solutions for ad hoc projects, as needed
• Support Quarterly Business Review (QBR) and Board of Directors (BoD) meetings as needed
• Perform other duties as assigned

Requirements

• Typically requires a minimum of 8 years of related experience with a bachelor's degree; or 6 years and a master's degree; or a PhD with 3 years' experience; or equivalent experience.
• Advanced degree in life sciences, pharmacology, or a related field preferred; an MBA or project management certification is a plus
• Demonstrated experience in program or project management within the biotech, pharmaceutical, or related life sciences industry
• Working knowledge of the drug development process, including preclinical, clinical, regulatory, and commercial requirements
• Experience supporting gene therapy, AAV vectors, or other advanced modality programs, and/or rare disease programs, strongly preferred
• Proven track record of successfully leading and managing cross-functional teams in the development and execution of complex development programs, preferably in gene therapy
• Up to 20% travel may be required

Skills and Attributes

• Self-starter with the ability to work independently and take initiative
• Strong organizational skills with the ability to manage a complex, multi-functional program
• Excellent leadership, communication, and interpersonal skills, with the ability to influence and collaborate effectively at all levels of the organization
• Strategic thinker with the ability to prioritize and make informed decisions in a fast-paced environment
• Strong problem-solving abilities and a proactive, critical-thinking approach to identifying and resolving issues
• Willingness to learn and collaborate in a dynamic team environment
• Excellent written and oral communication skills, including experience preparing materials for and presenting to senior leadership
• Proficient in Smartsheet, Office Timelines and/or other project management tools and software
• Proven ability to evaluate existing PMO tooling, workflows, and delivery frameworks; skilled at identifying operational bottlenecks and providing strategic recommendations to modernize and streamline processes
• Comfortable operating in a fast-paced, evolving company environment with the ability to adjust priorities as needed

Preferred Qualifications

• PMP certification or equivalent program/project management credential
• Experience supporting rare disease or CNS-focused gene therapy programs
• Familiarity with gene therapy-specific regulatory considerations
• Demonstrated experience leveraging AI-assisted features within modern program and portfolio management tools to automate workflows, synthesize project data, and enhance team productivity
• Experience with governance processes in a biotech or pharmaceutical organization (e.g., portfolio reviews, stage-gate processes)
• Familiarity with IND submission

For candidates based in the San Francisco Bay Area, the salary range for this position is $170,000 – $205,000.

For candidates based outside the San Francisco Bay Area, the salary range is $160,000 – $189,000.

Encoded considers a variety of factors when determining base compensation, including experience, qualifications, internal equity, and geographic location. Actual compensation will be determined based on relevant skills, experience, qualifications, internal equity, and business needs. This position may also be eligible for a discretionary annual bonus, discretionary stock-based long-term incentives, paid time off, and a benefits package.

• Comprehensive benefits package, including competitive employer premium contributions
• PTO, sick time and holiday pay
• Generous Parental Leave program
• Pre-tax medical and dependent care programs
• STD, LTD, Life and AD&D
• Team-building events
• Fully stocked micro-kitchen
• Fitness center at South San Francisco location

Encoded is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind. Encoded is committed to the principle of equal employment opportunity for all employees and to providing employees with a work environment free of discrimination and harassment. All employment decisions at Encoded are based on business needs, job requirements and individual qualifications, without regard to race, religion or belief, color, national origin, gender, status as a protected veteran, status as an individual with a disability, or any other status protected by the laws or regulations in the location in which we operate. Encoded will not tolerate discrimination or harassment based on any of these characteristics. Encoded encourages applicants of all ages.

If you need assistance or an accommodation due to a disability, you may call us at [phone].

The job description does not explicitly offer remote work. The role is based in South San Francisco, CA, and involves regular cross-functional team collaboration and leadership meetings, strongly implying an on-site or hybrid arrangement.

Is this role remote or on-site? The job description does not explicitly offer remote work. The role is based in South San Francisco, CA, and involves regular cross-functional team collaboration and leadership meetings, strongly implying an on-site or hybrid arrangement.

For candidates in the San Francisco Bay Area, the range is $170,000–$205,000. For candidates outside the Bay Area, the range is $160,000–$189,000. The role may also include a discretionary bonus and stock option grants.

What is the salary range for this position? For candidates in the San Francisco Bay Area, the range is $170,000–$205,000. For candidates outside the Bay Area, the range is $160,000–$189,000. The role may also include a discretionary bonus and stock option grants.

Typically 8 years with a bachelor's degree, 6 years with a master's, or 3 years with a PhD. Experience in gene therapy, AAV vectors, or rare disease programs is strongly preferred.

What experience is required for this role? Typically 8 years with a bachelor's degree, 6 years with a master's, or 3 years with a PhD. Experience in gene therapy, AAV vectors, or rare disease programs is strongly preferred.

Yes, up to 20% travel may be required as part of this role.

Is travel required for this position? Yes, up to 20% travel may be required as part of this role.

PMP certification is listed as a preferred qualification, not a hard requirement. An MBA or other project management credential is also noted as a plus.

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