He was a mission specialist aboard the Life and Microgravity Spacelab, launched in June 1996 on the space shuttle Columbia. In April 1998, he was payload commander on the Columbia mission to study the effects of microgravity on the brain and nervous system. In March 2002, he flew on Columbia to service the Hubble Space Telescope, making three space walks totalling more than 21 hours. In 2008, he flew aboard space shuttle Endeavour on the 25th shuttle/station assembly mission. Linnehan was selected as an astronaut in 1992.