The terminal for the River Line, with two tracks and two side platforms, is located across south Clinton Avenue from the main station building.

Rail service in Trenton dates back to the days of the Camden and Amboy Railroad, which built a station on East Street in 1837, until it was moved to the current site in 1863.

Amtrak took over intercity railroad service in 1971, but Penn Central continued to serve commuters, even as the station building closed in 1972.

NJ Transit Rail Operations took over the station when it acquired Conrail's New Jersey commuter lines in 1983, but the station continued to serve Amtrak as well as SEPTA Regional Rail to Philadelphia.

From 2006 to 2008, a major reconstruction project authorized by NJT took place with $46 million worth of federal aid, and $33 million worth of state funding that resulted in the current Trenton Transit Center.