The Vehicle Management Control System will be used to control all flight surfaces and perform overall vehicle management duties for the MQ-25 UAV.
The IFF product "ensures operation in contested environments by reliably identifying both coalition and enemy vehicles".
"BAE Systems leads the industry in high-integrity fly-by-wire and mission-critical IFF technologies" said Corin Beck, director of Military Aircraft Systems at BAE Systems.
"Our relationship with Boeing started more than four decades ago and has resulted in aircraft that have some of the most advanced avionics and reduced size transponders in the world."
The MQ-25 is the US Navy's first carrier-based UAV, and is designed to provide a "much-needed" refueling capability.
Boeing has been tasked with providing four MQ-25 aircraft to the US Navy for Initial Operational Capability by 2024.
"The MQ-25 program is vital because it will help the US Navy extend the range of the carrier air wing, and Boeing and our industry team is all in on delivering this capability," said Dave Bujold, Boeing's MQ-25 program director.
"The work we're doing is also foundational for the future of Boeing – where we're building autonomous systems from seabed to space."