Pioneering Medicines: Associate Director / Director, Clinical Operations

flagshippioneeringinc

Cambridge, MA USA · Cambridge · United States

Posted Jun 4, 2026

Other
Clinical Development

Job description

What if... We could harness the power of Flagship’s scientific platforms and create novel treatment options that benefit more patients, sooner?

Pioneering Medicines, an initiative of Flagship Pioneering, is building a world-class biopharmaceutical R&D capability focused on conceiving and developing life-changing treatments for patients by harnessing the power of Flagship's scientific platforms and applying those innovative approaches to serious diseases with unmet medical need. Unique to Pioneering Medicines’ approach is the opportunity to combine platforms to create truly novel and potentially transformative treatments. 

Position Summary:

Pioneering Medicines is seeking an Associate Director or Director, Clinical Development Operations to join our growing team and take direct ownership of one or more early-phase clinical programs.

This role is being created in direct response to the expansion of Pioneering Medicines' clinical portfolio. The ideal candidate thrives in a lean, high-ownership environment and is ready to step into full program stewardship from day one.

Key Responsibilities:

Clinical Program Ownership

Serve as the operational lead for one or more early-phase clinical trials (Phase 1/2), owning end-to-end program execution from study start-up through close-out and CSR.
Collaborate closely with the Clinical Development Team including clinical scientists, pharmacometricians, safety, biostatistics, data management, regulatory affairs, and quality.
Lead or contribute to the design of clinical trials and clinical development plans, including protocol development, operational feasibility assessments, country/site selection, and recruitment strategy.
Participate meaningfully in dose escalation meetings, DSMB preparations, IND/CTA submissions, and other key regulatory and governance milestones.
Prepare and present program operational updates to internal stakeholders; develop materials for investigator meetings and advisory boards.

Clinical Trial Execution

Lead site start-up, patient enrollment, monitoring, protocol compliance, and study close-out activities with a hands-on, accountability-driven approach.
Author and/or review clinical documents including protocols, IBs, ICFs, CSRs, pharmacy manuals, CRFs, DSURs, SAPs, and other trial-related materials.
Oversee clinical data systems and processes: CRF design and UAT, data review and discrepancy resolution, CRA training, and site performance oversight.
Build and maintain accurate trial timelines, trackers, and operational status reports; proactively escalate timeline, budget, or resource risks.
Manage trial budget including forecasting, tracking, and reconciliation; flag variances and develop mitigation plans.
Ensure timely collection of clinical data, samples, and lab results; maintain TMF quality and audit readiness.

CRO, Site & Vendor Management

Lead RFP processes for assigned program vendors; coordinate cross-functional bid defense meetings, complete scorecards, and support selection decisions.
Manage day-to-day relationships with CROs, clinical sites, IRBs, central labs, IWRS providers, and DSMBs to ensure high-quality, timely deliverables.
Review monitoring visit reports (MVRs), conduct oversight monitoring, and escalate issues related to site or CRO performance as needed.
Develop and implement action plans to address protocol compliance, safety, data quality, and administrative issues at investigational sites or with CROs.
Track and report on vendor KPIs, risk mitigation plans, and program milestones.

Organizational Contribution

Contribute to the development and continuous improvement of organizational processes, SOPs, templates, and operational standards.
Support team onboarding and knowledge transfer; may provide informal mentorship to junior colleagues or contractors over time.
Maintain current knowledge of ICH-GCP, FDA, EMA, and other applicable regulatory requirements; apply expertise to ensure trial compliance.

Qualifications:

Bachelor's degree or higher (MS, PharmD, PhD a plus) in life sciences or a related field preferred.
Minimum 10+ years of industry drug development experience, including:
At least 5 years of direct clinical trial management experience with clear program ownership.
Demonstrated experience executing early-phase clinical trials including FIH and IND/CTA-opening studies.
Experience at startups or small biotech companies highly valued.
Broad knowledge of drug development processes; strong working knowledge of ICH-GCP, FDA, EMA, and other global regulatory requirements.
Proven success managing multi-site global clinical trials including oversight of timelines, budgets, and vendors.
Deep experience with CRO and vendor selection, onboarding, and performance management.
Working knowledge of key clinical systems including EDC, CTMS, RTSM, and eTMF; prior TMF QC and audit readiness experience required.
Ability to operate effectively in lean, matrixed, fast-moving environments with a high degree of autonomy.
Excellent cross-functional collaboration and communication skills; strong project planning and problem-solving capabilities.
Experience in metabolic diseases, obesity, oncology and/or rare diseases highly desirable.
Willingness and ability to travel domestically and internationally up to 10%.

About Flagship

Flagship Pioneering is a scientific innovation engine that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps in human health, sustainability, and beyond.

What sets Flagship apart is our ability to advance biotechnology by uniting life science innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our team of scientists, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and create breakthroughs for the benefit of people and planet. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been named four times to Fast Company’s annual list of the World’s Most Innovative Companies.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $148,000 - $236,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Medicines currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Medicines's good faith estimate as of the date of publication and may be modified in the future.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.