He is the great-great-grandson of Frederick George Waterhouse, first curator of the South Australian Institute Museum, and naturalist of the John McDouall Stuart Expedition 1861-1862.
As a child, Thomas was fascinated by space. His father has described how he started building model rockets from cardboard and plastics. After completing his studies, Thomas accepted an offer from Lockheed in Atlanta. By 1990 he was the organization's principal aerodynamic scientist. His career continued in the field, steering towards more senior research positions.
Thomas was selected by NASA in March 1992 and reported to the Johnson Space Center in August 1992. In August 1993, following one year of training, he was appointed a member of the astronaut corps and was qualified for an assignment as a mission specialist on Space Shuttle flight crews.
While awaiting space flight assignment, Thomas supported shuttle launch and landing operations as an Astronaut Support Person (ASP) at the Kennedy Space Center. He also provided technical support to the Space Shuttle Main Engine project, the Solid Rocket Motor project and the External Tank project at the Marshall Space Flight Center. In June 1995, Thomas was named as payload commander for STS-77 and flew his first flight in space on Endeavour in May 1996. Although Paul D. Scully-Power had entered orbit as an oceanographer in 1985, Thomas was the first Australia-born professional astronaut to enter space.
He next trained at the Gagarin Cosmonaut Training Center in Star City, Russia in preparation for a long-duration flight. In 1998, he served as Board Engineer 2 aboard the Russian Space Station Mir for 130 days. From August 2001 to November 2003, Thomas served as Deputy Chief of the Astronaut Office. Thomas completed his fourth space flight on STS-114 and has logged over 177 days in space. He was working with issues for the Exploration Branch of the Astronaut Office until his retirement from NASA in February, 2014.
NASA officially announced Thomas' retirement on 20 June 2014, which took effect on 1 March 2014, after 22 years with the space agency
STS-77 was a mission during which the crew deployed two satellites, tested a large inflatable space structure on orbit and conducted a variety of scientific experiments in a Spacehab laboratory module carried in Endeavour's payload bay. The flight was launched from the Kennedy Space Center on 19 May 1996 and completed 160 orbits 153 nautical miles (283 km) above the Earth while traveling 4.1 million miles and logging 240 hours and 39 minutes in space.