Two trains collided near Brannan Street and The Embarcadero, Muni officials wrote on Twitter at 1:43 p.m.
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Fire crews also arrived on the scene to assist with medical care. A San Francisco Fire Department spokesperson said four people have been transported to hospitals, while three are being assessed and all are in stable condition.
The San Francisco Department of Emergency Management advised motorists to avoid the area and to expect traffic delays.
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Muni officials said the T-Third and N-Judah lines are delayed due to the collision. Bus shuttles will support riders on both lines, and residents should consider taking the 15-Bayview Hunters Point Express, 30-Stockton or 45-Union/Stockton bus lines as an alternative.