Senior UAS Systems Integration Engineer II

flagshippioneeringinc; Boulder (CO); On-site; USD 110,000 - 150,000; Full time

Job summary

Flagship Pioneering is seeking an experienced UAS Systems Integration Engineer II to join our hardware team. This role sits at the intersection of firmware, electronics, and airframe design, driving the autopilot stack, airframe integration, and C2 link from concept to field-ready deployment.

You will work in a small, high-caliber team to develop end-to-end systems capable of precision scientific missions in demanding international environments.

Qualifications

• Bachelor's or Master's degree in aerospace, electrical, mechanical, or computer science (or equivalent hands-on experience).
• BS + 2-4 or MS + 0-2 years hands-on hardware/software systems integration experience in real-mission or production contexts.
• Proficiency in C++ and Python, with experience reading, modifying ArduPilot code; MAVLink familiarity.

Responsibilities

• Configure, tune autopilot firmware for fixed-wing airframes using ArduPlane.
• Read, modify, and debug ArduPilot source code (C++) to extend autopilot capabilities and resolve anomalies.
• Design, build, and iterate fixed-wing airframes for payload capacity, endurance, and resilience.
• Support flight test campaigns with pre-flight checks, telemetry setup, and rapid fixes between flights.
• Develop C2 link architecture, RF link budgets, electronics integration, and spectrum strategies for long-range BVLOS.
• Design and implement custom ground station software and mission-planning interfaces.
• Integrate and validate onboard science payloads and sensors for data integrity and mission performance.
• Analyze flight logs to diagnose issues and drive improvements in reliability.
• Design and fabricate electronics, including PCB layout for power distribution and avionics integration.
• Document designs, tests, firmware changes, and component specs for a scalable knowledge base.

Skills

C++

Python

ArduPilot

MAVLink

GCS tooling

RF design

PCB design

Systems integration

Education

Bachelor's or Master's in a relevant field

Tools

ArduPlane

ArduPilot

PX4

MAVLink

GCS tools

Job description

COMPANY DESCRIPTION

Flagship Pioneering is a platform innovation company 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. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform 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 twice named to Fast Company's annual list of the World's Most Innovative Companies.

THE ROLE

We are seeking a UAS Systems Integration Engineer II to join our growing hardware team. This is a deeply technical, hands-on engineering role for someone who lives at the intersection of firmware, electronics, and airframe design. You will help drive the development of the technical architecture of our fixed-wing UAV platform - co-developing the autopilot stack, airframe, payload integration, and C2 link from the ground up. Working within a small, high-caliber team, you will drive the system from early prototype toward a hardened, field-deployable platform capable of executing precision scientific missions in demanding international environments. The ideal candidate brings end-to-end systems thinking and a builder's instinct - equally comfortable in CAD, oscilloscope traces, and firmware source code.

KEY RESPONSIBILITIES

• Configure, tune, and iterate on autopilot firmware for fixed-wing airframes, including PID tuning, failsafe logic, auto modes, and mission scripting using ArduPlane;
• Read, modify, and debug ArduPilot source code (C++) to extend autopilot capabilities, implement custom behaviors, and resolve vehicle-level anomalies;
• Design, build, and iterate on fixed-wing airframes across aerodynamics, structures, and propulsion integration - optimized for payload capacity, endurance, and operational resilience;
• Support flight test campaigns alongside flight operations - pre-flight vehicle readiness checks, ground station and telemetry setup, in-field troubleshooting, and rapid turnaround of firmware and hardware fixes between flights;
• Develop C2 link architecture, RF link budgets, electronics integration, and spectrum compliance strategies for long-range BVLOS operations;
• Design and implement custom ground station software and user interfaces to support mission planning, real-time monitoring, and post-flight analysis;
• Integrate and validate onboard science payloads and sensors, ensuring electrical compatibility, data integrity, and mission performance;
• Analyze flight logs (MAVExplorer, Flight Review) to diagnose anomalies, validate performance models, and drive systematic improvements to vehicle reliability;
• Design and fabricate custom electronics, including PCB layout for power distribution, sensor interfacing, and avionics integration;
• Document designs, test results, firmware change logs, and component specifications to build a scalable engineering knowledge base for the drone program.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS

• Bachelor's or Master's degree in aerospace engineering, electrical engineering, mechanical engineering, computer science, or a closely related field; equivalent hands-on experience will be considered.
• BS + 2-4 or MS + 0-2 years of hands-on hardware/software systems integration experience required, in real-mission or production contexts;
• Proficiency in C++ and Python, with demonstrated experience reading, modifying, and debugging ArduPilot source code; strong familiarity with MAVLink protocol and GCS tooling;
• Hands-on experience with ArduPilot or PX4 based autopilot systems, preferably in production-ready or real-mission contexts;
• Experience with RF link design, C2 spectrum compliance, antenna selection, and electronics integration for long-range UAV systems;
• Electronics design and integration experience required; PCB design and fabrication experience is a strong plus;
• FAA Part 107 Remote Pi