Marshburn joined NASA in November 1994, serving as a flight surgeon at Johnson Space Center in Houston, Texas. He was assigned to Space Shuttle Medical Operations and to the joint US/Russian Space Program. From February 1996 to May 1997 he served as a flight surgeon for NASA personnel deployed to the Yuri Gagarin Cosmonauts Training Center, Star City, Russia, followed by work in the Center for Flight Control in Korolyov, Russia, in support of the NASA Expedition 4 to the Mir Space Station. From July 1997 to August 1998 he was co-chair of Medical Operations for the Shuttle–Mir Program. From 1998 to 2000, he was deputy Flight Surgeon for Neuronal (STS-98) and lead Flight Surgeon for the STS-101 mission to the International Space Station (ISS).