In addition to local services, the following long-distance trains serve Hakodate Station.

The following services ended in March 2016 due to the Hokkaido Shinkansen's opening: From Shin-Hakodate-Hokuto Station to Shin-Aomori Station, which takes a similar route of the Hakuchō\Super Hakuchō.

All services go through to Tokyo station, which means the two former sleeper trains had to be discontinued due to the Hokkaido Shinkansen's opening.

An extension to Sapporo is currently under construction and will be completed in fiscal 2031.

"Relay" shuttle services (Hakodate liner) using three-car 733 series electric trains operate between Hakodate and Shin-Hakodate-Hokuto Station.