The man, described as in his 50s, was struck by an outbound M-Ocean View train around 11:45 a.m., Rose said.
He suffered severe leg injuries and was taken to a hospital, where he died, Rose said.
San Francisco police have responded to the Civic Center station to investigate the incident, he said.
Rose said it is not yet clear why the man was on the tracks.
After the collision, Muni Metro service was shut down between the Embarcadero and West Portal stations, and bus shuttles were set up to carry riders along that stretch.
Rose said around 1:20 p.m. that underground service was expected to resume shortly.
