The man was discovered Sunday night after authorities responded to reports that a rider was stuck in an elevator.
The rider later told authorities that he heard noise while taking the elevator up at the bustling Montgomery Street station, transit police Lt. Michael Hayes told The Associated Press.
"The rider said he had been riding up to the concourse when he heard a crunching sound, followed by a scream," Hayes said. "Then the elevator stalled."
A man was later found dead on top of the elevator along with personal belongings that apparently included bedding, transit spokeswoman Luna Salaver said.
"We don't understand why anyone would seek refuge in an elevator shaft. It is disturbing, upsetting and highly unusual," Salaver said. "This has never happened before in our 40 years of service."
Authorities suspect the man was homeless, and it was unknown how long he had been inside the elevator, Salaver said. He had no identification when he was found.
BART ticket agents and police conduct sweeps inside stations prior to closing time. Typically, homeless and transient people camp overnight outside a station's gate to get away from the elements, Salaver said.
The incident is under investigation by transit police, and inspectors with Cal OSHA were expected to conduct a separate probe. The elevator could be back in service by March 20, Salaver said.
The death is not considered suspicious, Hayes said.
The Associated Press contributed to this report.