He was the first Japanese mission specialist on a space shuttle mission when he flew on Endeavour in January 1996 to retrieve the Space Flyer Unit, an uncrewed space experiment platform, launched from Japan. He also flew on the Discovery mission in October 2000 to expand the International Space Station. From March to July 2009, Wakata flew as the first resident ISS crew member from Japan, and served as a flight engineer and the JAXA science officer on the crews of Expeditions 18, 19, and 20. He returned to the ISS in November 2013, serving as flight engineer on Expedition 38 and as commander of ISS Expedition 39 in March 2014 (becaming the first Japanese ISS commander). Wakata was selected as an astronaut with the National Space Development Agency in 1992 and assigned to NASA's Johnson Space Center for training in the same year.