He began his NASA career at the Johnson Space Center (JSC), Houston, Texas, in 1966 as an engineer in Flight Operations for the Apollo Program.

In 1981 Honeycutt served as technical assistant to the associate administrator for the Space Transportation System, NASA Headquarters.

From 1986-1987, he was special assistant to the NASA Associate Administrator for Space Flight, and coordinated Presidential Commission and Congressional activities relative to the Challenger accident.

In this role Honeycutt was responsible for engineering management and technical direction of pre-flight, launch, landing and recovery activities for Space Shuttle vehicles.

[2][needs update] On 22 September 2008, he joined Odyssey Moon where he was named president and was responsible for all programs and commercial launch operations.