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Encoded Therapeutics

Clinical Program Manager (Gene Therapy)

Remote, United States

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Job details

Posting language: English
Posted: Oct 26, 2026

Original job description

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. Reporting to the Senior Director of Clinical Operations, the Clinical Program Manager will be responsible for leading the operational strategy and execution for a novel clinical-stage gene therapy program. Working with the Medical Monitor, cross-functional trial teams, and external experts, the CPM will drive clinical trial planning, protocol development, site and vendor selection, and study startup to support corporate development goals.

The specific responsibilities of this position include:

Accountable for end-to-end operational execution of a novel gene therapy clinical program, managing cross-functional alignment, trial budgets, and project timelines from protocol concept through to Clinical Study Report (CSR) completion.
Develop documents and procedures required to conduct clinical studies, including protocols, informed consent forms, investigator brochures, case report forms, study procedure manuals.
Identify and interpret risks, and implement mitigation strategies/corrective actions to address them
Develop and manage clinical study timelines consistent with the company’s goals
Develop and manage study budgets
Select study investigators and evaluate adequacy to perform research and meet study timelines.
Build relationships with clinical sites
Managing studies to meet enrollment goals
Contribute to development of key regulatory documents such as INDs and CTAs
Conduct oversight monitoring activities, as needed
Partner with data management colleagues to lead study data review activities
Provide oversight of the ongoing maintenance of the Trial Master File
Contribute to development of clinical study reports
Monitor compliance with all company standard operating procedures (SOPs), GCP, FDA and applicable international regulations concerning clinical activities
Create and implement Study Management plans and processes in compliance with industry standards and regulatory requirements
Represent clinical operations in cross-functional initiatives and act on behalf of team, as assigned by management
Provide direct line management, oversight, and operational guidance to contract Clinical Operations personnel (e.g., contract CTMs, CRAs, or CTAs).
Travel internationally and domestically as required
Minimum of 8 years of pharma/biotech clinical operations experience with a Bachelor’s degree in a relevant scientific discipline or equivalent (6 years with a Master’s, or 3 years with a PhD). Requires proven end-to-end management of complex clinical trials, with gene therapy experience strongly preferred
Thorough knowledge and understanding of FDA and ICH Guidelines, Good Clinical Practices (GCP), medical terminology, and clinical trials
Detailed understanding of all aspects of clinical protocol design and implementation and overall drug development
Outstanding project management experience
History of success selecting and managing vendors with performance standards
Strong financial acumen measured by outstanding track record of building budgets and managing expenses to budget.
Proficiency with word processing, spreadsheet, database, and presentation software and with filing (archiving) systems
Demonstrated problem solving abilities and strong organizational skills
Outstanding written communication skills including writing technical documents, such as protocols, protocol amendments, informed consent, and other trial-related documents
Must be self-motivating, prioritize and manage a large volume of work, and show attention to detail
Strong interpersonal skills with reputation for collaboration with colleagues; influencing up, down and across the organization
Excellent verbal and written communication skills required including writing clearly and summarize information effectively

For candidates based in the San Francisco Bay Area the salary range for this position is 160,000 - 180,000 For candidates based outside the San Francisco Bay Area, the salary range is 145,000 - 165,000 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
Meaningful stock option grants
PTO, sick time and holiday pay
Generous Parental Leave program
Pre-tax medical and dependent care programs
STD, LTD, Life and AD&D
Professional development opportunities
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 +1 650-491-0272.

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