Apt joined NASA in 1980 as a research scientist. In 1986, he became an astronaut. He has flown on four space missions and has logged over 847 hours.
In 1991, Apt flew aboard shuttle Atlantis where he made a spacewalk. In 1992, he flew aboard shuttle Endeavour and performed life science experiments. In 1994, Apt was part of the first Space Radar Laboratory. This lab studied the Earth. In 1996, Apt flew aboard shuttle Atlantis and visited the Russian Mir space station.