About Pioneering Intelligence

Pioneering Intelligence builds on Flagship Pioneering's legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship's integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

The Role

The Pioneering Intelligence team at Flagship Pioneering builds the digital and AI foundation that accelerates the creation and growth of our companies. We are seeking a Vice President of Engineering to lead a medium sized team of Principal Software Engineers, each operating as the technical authority for their own product area.

This is a non-traditional engineering leadership role. Rather than managing a layered organization, you will build and support a team composed entirely of senior individual contributors operating as technical leads at the highest level. Each engineer owns end-to-end technical decisions, builds hands-on, and engages directly with scientific users. Your job is not to manage their work but to set the conditions in which exceptional engineers do their best work, remove obstacles, raise the collective bar, and translate technical strategy into organizational direction.

You remain technically active. You will contribute to architectural decisions, review complex system designs, and stay close enough to the work to lead credibly. You spend roughly 25% of your time in hands-on technical work. The rest is spent on strategy, people, and organizational leadership: building the team, aligning with product leadership, representing the function to senior stakeholders, and driving the conditions for fast, high-quality delivery across the portfolio.

The model is intentionally fluid. Principal Engineers on this team may move between pure IC work and the formal coordination of other resources as project needs evolve, including the management of fully embedded software engineering contractors. It is the VP who balances resources across all teams and projects, in close collaboration with product and strategy leads, ensuring the right people are working on the right things at the right time.

You will work in close partnership with product and strategy leads and alongside a team of peers who expect the same rigor and accountability from you that you expect from them.

Key Responsibilities

• Lead and develop a team of approximately five Principal Software Engineers, each owning technical authority for their own product area
• Set technical strategy and architectural direction for the AI and digital platform, making or ratifying the most consequential build-vs-buy and system design decisions
• Stay technically active: contribute to architectural reviews, design complex systems, and maintain the credibility to lead a team of principal-level engineers
• Build and maintain the team itself: hire exceptional engineers, develop their careers, and create a culture where the floor is principal-level performance
• Represent engineering to product leadership, senior stakeholders, and across the Flagship ecosystem, translating technical direction into business impact
• Balance resources across all teams and projects in close collaboration with product and strategy leads, including decisions about when Principal Engineers take on formal coordination of embedded SWE contractors versus pure IC work
• Drive delivery across the portfolio by removing blockers, resolving cross-team dependencies, and ensuring the team ships with speed and quality
• Model and advance an AI-native engineering culture, including the use of tools like Claude Code as organizational force multipliers

Professional Experience and Qualifications

Experiences

• Has led a team of senior individual contributors or principal-level engineers, ideally in a lean, high-velocity organization where the team was small and the scope was large
• Has served as the technical authority on a complex, production-grade system, not as a manager who delegates the hard parts, but as an engineer who owned them
• Has built and scaled engineering organizations in ambiguous, fast-moving environments, ideally at a startup or within a high-autonomy team inside a larger organization
• Has worked closely with scientific or domain-expert users and understands how to build products that serve researchers, not just operators
• Has hired and developed principal or staff-level engineers, with a track record of raising the technical bar of a team over time

Skills

• Technically credible at the system design level: can evaluate architectural decisions, identify risk in complex designs, and contribute meaningfully to the hardest engineering conversations
• Leads through clarity: sets direction, makes decisions, and communicates tradeoffs without requiring repeated alignment
• Builds teams, not just products: knows how to hire exceptionally, develop senior talent, and create conditions where strong engineers stay and grow
• Fluent in AI-native ways of working and comfortable leading a team that uses tools like Claude Code as a core part of their engineering practice
• Writes with the same precision they expect from their engineers: strategy docs, architectural reviews, and hiring rubrics that don't require a follow-up meeting

Traits

• Strategic and hands-on at the same time: comfortable moving between organizational leadership and technical depth without losing credibility in either
• High standards without bureaucracy: holds the team to an exceptional bar without slowing them down with process for its own sake
• Founder-minded: attracted to ambiguity, motivated by impact, and able to build clarity from uncertainty rather than waiting for it to arrive
• Direct and decisive: makes calls with available information, owns the outcomes, and creates psychological safety for their team to do the same
• Multiplier, not bottleneck: earns trust by making the people around them better, not by centralizing decisions

Why Pioneering Intelligence?

• Lead a team of principal-level engineers where the work is genuinely hard and the people are genuinely exceptional
• Shape the technical strategy of an AI-native platform at the intersection of cutting-edge AI and life sciences
• Operate with the autonomy and organizational support to build the team and culture you believe in
• Work at the frontier of AI-augmented engineering, where the tools are state-of-the-art and the model of how software gets built is being reinvented
• Collaborate with visionary scientists, founders, and builders across Flagship's ecosystem
• Competitive compensation and benefits, including equity, commensurate with experience

About Flagship Pioneering

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies 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 twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.

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 $313,000 - $400,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.