Before Grödingebanan [sv] was constructed in the 1990s, Södertälje hamn was the main train station in Södertälje for national and regional trains.

All commuter trains between Stockholm and Södertälje centrum need to charge direction in Södertälje hamn, due to the track layout.

There are three commuter rail lines through Södertälje hamn.

J40 and J41 go from Södertälje centrum via Stockholm City Station to Uppsala and Märsta respectively.

The station is within walking distance to the Port of Södertälje vicinity as well as the headquarters and main factory of Scania AB.