He has over 5,000 hours of flying experience in a variety of aircraft, primarily the T-38, F-4, F-15, and F-16.

McMonagle flew as a mission specialist aboard the Space Shuttle Discovery on Mission STS-39. This eight-day unclassified Department of Defense mission launched from Kennedy Space Center on April 28, 1991, and landed there on May 6, 1991. During this highly successful mission, the seven-man crew worked around-the-clock in a two-shift operation. They deployed, operated, and retrieved a remotely controlled spacecraft and conducted several science experiments to include research of both natural and induced phenomena in the Earth's atmosphere. McMonagle was the pilot during his shift of operations, responsible for flying the Space Shuttle through several maneuvers and operating Discovery's systems in support of science experiments. Mission duration was 199 hours and 22 minutes.

McMonagle served as pilot on STS-54 (January 13-19, 1993) aboard the Space Shuttle Endeavour. The six-day mission featured the deployment of a Tracking and Data Relay Satellite (TDRS), the collection of information about celestial x-rays using a Diffuse X-Ray Spectrometer (DXS), a 4 hour and 20 minute space walk by two fellow crewmen to explore the limits of human performance in working outside the spacecraft, and the demonstration of physics principles of common toys to an interactive audience of elementary school students across the United States. McMonagle executed over 100 Orbiter maneuvers to properly point the DXS. In preparation for future space station operations, McMonagle conducted the first on-orbit shutdown and restart of one of the three electricity-producing fuel cells on the Orbiter. Mission duration was 143 hours and 38 minutes.

McMonagle commanded a crew of six aboard Space Shuttle Atlantis on the STS-66 Atmospheric Laboratory for Applications and Science-3 mission (November 3-14, 1994). ATLAS-3 was part of an ongoing program to determine the Earth's energy balance and atmospheric change over an 11-year solar cycle. Eight instruments in Atlantis' cargo bay measured the total and spectral output of the sun and chemical constituents in the atmosphere including measurements of global ozone coverage. The mission also included the second in a series of four German-sponsored flights of a Shuttle Pallet Satellite (SPAS). Named CRISTA/SPAS, the satellite was deployed for 8-days carrying two instruments (CRISTA and MAHRSI) which measured small scale dynamic variations in the middle atmosphere and unique chemicals which affect ozone chemistry. During the rendezvous with SPAS, McMonagle demonstrated the first "R-bar" approach flying up from below as opposed to the traditional approach from ahead of a rendezvous target. The 11-day mission was completed with McMonagle's landing the Atlantis at Edwards Air Force Base after 175 orbits of the Earth. Mission duration was 262 hours and 34 minutes.

McMonagle currently serves as the Director, EVA Project Office, Johnson Space Center.