The unmanned aircraft successfully launched at 11:36 a.m. PT and separated from the B-52 Bomber as planned, but 16 seconds later, a fault was identified with one of the cruise control fins, and the cruiser crashed.
"It is unfortunate that a problem with this subsystem caused a termination before we could light the Scramjet engine," said program manager Charlie Brink in a statement.
The aircraft was designed to fly six times the speed of sound. The technology could someday take people across the world in less than an hour.
One of the four X51A vehicles remain, according to the Air Force. Officials have not yet decided when or if that vehicle will fly.