The train derailed at about 12:45 p.m. at Winchester Boulevard between state Highway 85 and Lark Avenue, Los Gatos police Sgt. Randy Rimple said.
No injuries were reported, Rimple said.
The train, which consisted of two engines and 11 cars, derailed as it was veering left at a curve, according to Rimple.
The wheels of the engine cars came off the tracks, causing the three cars behind to partially derail, Rimple said.
Crews were able to get the first engine car back on the rail by 2:45 p.m., but the remaining engine had not been re-railed as of 4:30 p.m., according to Rimple.
Once all the cars are back on the rail, crews will then have to repair the ground and rails, Rimple said.
The half-mile stretch of Winchester Boulevard between state Highway 85 and Lark Avenue is expected to remain closed until Saturday morning, Rimple said.
Commuter trains should not be affected by the derailment, Rimple said.