A modified Boeing 747 with the shuttle mounted on its back touched down on the shuttle landing strip around 8:25 a.m. EDT after taking off from a refueling stop in Kentucky.
The jet made several stops on its cross-country trip. On Monday, it landed in Fort Campbell, Ky., after stops at Offutt Air Force Base in Nebraska and Amarillo, Texas.
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Atlantis, carrying seven astronauts, landed June 22 at Edwards Air Force Base in California after a 14-day construction mission at the international space station.
Bad weather at the Florida launch site forced NASA to divert to the shuttle's alternate landing site in California. NASA prefers to land shuttles in Florida to avoid the more than $1.7 million price tag to transport them back.
The vehicle will be cleaned and refurbished before being readied for its next trip, scheduled for December. The next scheduled mission will send Endeavour to the space station on Aug. 7.