While the spacecraft cleared the launch pad, the Super Heavy booster carrying it failed to separate from the second stage and subsequently exploded.
The rocket lifted off at 9:33 a.m. EDT and reached the altitude where stage separation was meant to take place.
While the booster stage was supposed to separate to guide itself back to Earth, an as-of-yet-undetermined malfunction caused the separation to fail about three minutes into the flight.
The entire platform rotated before eventually breaking up in what SpaceX commentators called a "rapid unscheduled disassembly."
On Friday, the FAA cleared the Starship for launch, saying "after a comprehensive license evaluation process, the FAA determined SpaceX met all safety, environmental, policy, payload, airspace integration and financial responsibility."
But after Thursday's events, the FAA said Starship will be grounded until an investigation can make sure "any system, process, or procedure related to the mishap does not affect public safety."
The highly anticipated test flight represented a crucial step toward sending a manned mission back to the moon and later to Mars.
SpaceX founder and CEO Elon Musk previously had stated that he believed the test flight had a 50% chance of success. NASA Administrator Bill Nelson took an optimistic view of the launch despite the destruction of the Starship and its launch platform.
"Congrats to SpaceX on Starship's first integrated flight test! Every great achievement throughout history has demanded some level of calculated risk, because with great risk comes great reward. Looking forward to all that SpaceX learns, to the next test flight - and beyond," Nelson tweeted Thursday.
The rocket will eventually be one of the largest vehicles ever sent into space, able to carry crew and cargo simultaneously.
The Starship and Super Heavy stack is 394 feet tall. SpaceX constructed a nearly 500-foot tall launch and catch tower at the Starship base in Boca Chica, Texas for its launch.
A previous launch attempt was scrubbed on Monday when a pressurization issue with the first stage was reported about 9 minutes before launch. NASA Space Flight reported a stuck valve was the issue. SpaceX then shifted focus and treated the pre-launch process as a wet dress rehearsal, Space.com reported.
"The point of the countdown is to allow the teams to progress that T-zero time in a coordinated fashion and really to unveil any issues prior to the ignition sequence. So the countdown did its job today," Kate Tice, host of SpaceX launch coverage and manager of SpaceX Quality Systems Engineering, said during that previous launch-attempt broadcast.
At the time, SpaceX said a successful test of the spacecraft would be measured by "how much we can learn."
Starship's six Raptor engines were meant to ignite seconds after separation and to keep running for more than 6 minutes before cutting off.
Had stage separation been successful, the Starship was meant to coast for most of the remainder of the estimated 90-minute flight before descending and splashing down in the Pacific Ocean off the coast of Kauai, Hawaii. The spacecraft was not meant to go into full orbit but to reach low-Earth orbit, and re-enter about 77 minutes after launch.
The Super Heavy booster, equipped with 33 Raptor engines, would be required to push Starship into orbit. Together, the engines would generate an estimated 16.5 million pounds of force. The engines burn liquid oxygen and liquid methane, which Space.com reported can be produced on Mars.
SpaceX commentators pointed out that it appeared three of the 33 Raptor engines on the booster stage either did not ignite or stopped working.
In February, Raptor engines were test-fired, with 31 of 33 on the Booster 7 working.
SpaceX founder Elon Musk at the time declared 31 engines would be enough to reach orbit.
Thursday's launch, despite the failure of stage separation, allowed SpaceX to test several systems in action.
"SpaceX intends to collect as much data as possible during flight to quantify entry dynamics and better understand what the vehicle experiences in a flight regime that is extremely difficult to accurately predict or replicate computationally," SpaceX said of its objectives in a document submitted to the FAA.
In February, SpaceX launched 21 Starlink V2 Mini satellites into orbit, but the satellites deorbited sooner than expected. SpaceX then swapped the V2 out in favor of the Starlink V1.5 model in a launch in March.
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