Police received the report of a person in the inbound tunnel around 3:05 p.m.
Officers responded and found a deceased person just east of the Castro Street station.
The incident is being investigated as a collision, police said.
Muni spokesman Paul Rose said the agency is now working with police to pull video footage of the area.
The incident is causing major delays in the subway system and on light-rail lines and passengers are being advised to take alternate routes to their destinations.
Bus shuttles are providing service between West Portal and Van Ness stations and BART will be honoring Muni fares.