The space plane, known as the X-37B, landed at Vandenberg Air Force Base on the Southern California coast on Friday after circling the Earth for 674 days.
What the shuttle was doing during that time remains a mystery.
The Air Force says the space planes, also known as Orbital Test Vehicles, “perform risk reduction, experimentation and concept-of-operations development for reusable space vehicle technologies”.
Others, including the Secure World Foundation, a nonprofit group that promotes the peaceful exploration of space, speculate that the secrecy is almost certainly tied to the presence of national intelligence-related hardware being tested or evaluated.
Costs associated with the programme are also classified.
Upon landing of the latest mission, the Air Force simply said the aircraft had been conducting “on-orbit experiments”.
It was the second flight for this X-37B. The same plane circled the planet for more than seven months in 2010. A second X-37B spacecraft blasted off in March 2011 and spent more than a year in orbit.
At 29ft (8 metres) long, the Boeing-built planes are about one-quarter the size of NASA’s old space shuttles.
They are equipped with solar panels that unfurl to charge its batteries once in orbit.
The Air Force said it plans to launch the fourth X-37B mission from Cape Canaveral, Florida, next year.