Wakata was born in Ōmiya, Saitama, Japan, earned a Bachelor of Science degree in Aeronautical Engineering in 1987, a Master of Science degree in Applied Mechanics in 1989, and a Doctorate in Aerospace Engineering in 2004 from Kyushu University. He worked as a structural engineer for Japan Airlines.

Wakata was selected by the National Space Development Agency of Japan (NASDA) (now JAXA) as an astronaut candidate in 1992, and trained at NASA’s Johnson Space Center. Wakata has held a number of assignments, and during STS-85, Wakata acted as NASDA Assistant Payload Operations Director for the Manipulator Flight Demonstration, a robotic arm experiment for the Japanese Experiment Module of the International Space Station (ISS). In December 2000, he became a NASA robotics instructor astronaut. In July 2006, he served as commander of the 10th NASA Extreme Environment Mission Operations (NEEMO) mission, a seven-day undersea expedition at the National Oceanic and Atmospheric Administration’s Aquarius laboratory located off the coast of Florida. In August 2006, he started flight engineer training for Russian Soyuz spacecraft in preparation for a long-duration stay on the ISS.

Wakata first flew aboard STS-72 in 1996, and then returned to space on STS-92 in 2000. Wakata was stationed at the International Space Station (ISS) and returned to earth aboard Endeavour with the STS-127 crew on July 31, 2009. On Nov 7, 2013 Wataka returned to the ISS aboard Soyuz TMA-11M for a 6-month mission covering Expeditions 38 and 39. He became the ISS commander for the last two months of that mission on Expedition 39.

In February 2007, Wakata was assigned as a flight engineer to ISS Expedition 18, scheduled to begin in winter of 2008. He launched with the crew of STS-119 and was the first resident station crew member from the Japanese Aerospace Exploration Agency (JAXA). He served as Flight Engineer 2 on Expedition 18, Expedition 19 and Expedition 20, before returning home as a Mission Specialist on STS-127.

As an experiment on the station, he wore the same special underpants for a month without washing them. Wakata returned to Earth in July 2009 aboard Endeavour with the STS-127 crew after being a flight engineer on the station. American and Canadian astronauts aboard STS-127 delivered and installed the final two components of the Japanese Experiment Module: the Exposed Facility (JEM-EF), and the Exposed Section (JEM-ES).

Wakata launched on Soyuz TMA-11M to the International Space Station in November 2013. During Expedition 38 and Expedition 39, Kirobo—who had the mission to serve as a companion robot to the astronaut—worked closely with Wakata, conducting experiments in space through verbal orders from the astronaut. One of the experiments was the first-ever human-robot conversation in space. Wakata arrived on the International Space Station as part of Expedition 38 in late 2013. He became the commander of the International Space Station with Expedition 39, in March 2014. This marked the first time a Japanese astronaut became ISS station commander, and only the third time an astronaut of neither Russian nor American citizenship served as station commander. Wakata returned to Earth on May 13, 2014.