The experimental X-51A Waverider failed in its bid to reach Mach 5, or around 3,800 mph.
The craft separated as planned from its B-52 mother ship in flight over the Pacific Ocean above the Point Mugu Naval Air Test Range in California, but things quickly went wrong after that, an Air Force statement said.
"The X-51 safely separated from the B-52 and the rocket booster fired as planned. However after 16 seconds, a fault was identified with one of the cruiser control fins. Once the X-51 separated from the rocket booster, approximately 15 seconds later, the cruiser was not able to maintain control due to the faulty control fin and was lost," the statement said.
The flight had been intended to last 5 minutes, CNET reported.
"It is unfortunate that a problem with this subsystem caused a termination before we could light the scramjet engine," Charlie Brink, X-51A program manager for Air Force Research Laboratory, said in a statement.