Principal Engineer, Agentic AI Platform Orchestration

Flagship Pioneering, Inc.

Cambridge (MA)

On-site

USD 188,000 - 258,000

Full time

14 days+

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Job summary

Flagship Pioneering, Inc. is seeking a Principal Software Engineer to own the durable agentic platform that powers autonomous scientific workflows.

You will architect the end-to-end orchestration layer, set standards, and mentor cross-disciplinary teams of AI scientists, engineers, and domain experts, turning frontier agent patterns into reusable infrastructure. The role blends hands-on architectural leadership with production-scale delivery, focusing on reliability, cost-efficiency, and

Qualifications

B.S. or M.S. in Computer Science, Engineering, or a related field, with 10+ years of professional software development experience.
Demonstrated track record architecting and maintaining large-scale distributed systems in production at technology companies.
Deep expertise in workflow orchestration and event-driven architecture, including stateful execution, idempotency, durable retries, and replay.
Strong cloud-native engineering on AWS with infrastructure-as-code, containerization, and autoscaling.
Proven ability to take systems from prototype to hardened, observable, operationally excellent production.
Experience designing SDKs, APIs, and data contracts that serve multiple downstream teams.
Excellent communication skills and the ability to build organizational consensus around platform decisions.
Collaborative and empathetic working style: listens to understand the needs of scientists, engineers, and downstream teams, and leads through influence.
Proven track record setting technical strategy and direction for a growing engineering organization, and mentoring engineers in a fast-moving environment.

Responsibilities

Own the agentic platform end to end, from research prototype to production, building the durable orchestration layer for long-running, multi-stage scientific workflows.
Architect workflow orchestration, evaluation frameworks, and event-driven distributed systems that deliver scale, resilience, and reliability.
Define SDK abstractions and API contracts between model and agent outputs and downstream consumers, decoupling rapid model iteration from product stability and reducing integration friction across teams.
Deliver infrastructure-as-code reference implementations (AWS CDK, Terraform, containerized services) and transform exploratory AI proof-of-concepts into hardened, reusable patterns adopted across product domains.
Own platform cost-efficiency and scalability while preserving the performance and accuracy that our experiments and end users require.
Explore and template agent design and deployment patterns, and set technical standards, code quality, and architectural direction for the platform.
Partner across teams to align on integration points, dependency timelines, and delivery, and mentor engineers and scientists.