Authorities responded at 7:26 a.m. to a report of a male on the inbound tracks at the Montgomery station, fire department spokeswoman Mindy Talmadge said.
The male was apparently walking in the tunnel between the Montgomery and Embarcadero stations when he was struck by the Muni vehicle, Muni spokesman Paul Rose said.
He was pronounced dead at the scene.
Muni Metro service was suspended in the subway between the Embarcadero and West Portal stations while crews responded to the scene. Service resumed at about 10:20 a.m., Rose said.
Bus shuttles took passengers to their destinations along the affected light-rail lines during the shutdown, he said.
BART was also allowing riders with Muni passes to board BART trains between the Balboa Park and Embarcadero stations in San Francisco during the disruption, BART spokesman Jim Allison said.
The operator of the Muni light-rail vehicle has been placed on non-driving status pending an investigation into the incident and will undergo alcohol and drug testing, as is standard procedure, according to Rose.