The station and all trains calling here are operated by Great Northern (with service to and from London King's Cross.)

A spur connecting the harbour was opened in 1849, and at one point was a complicated network of lines, boasting two swing bridges, serving premises on and around the town's South Quay.

[7][8] The railway was initially not welcomed by the port authorities in King's Lynn; they predicted that sea-bound trade would decline, and were later proved correct when through-trains to London ended up carrying the majority of freight to the capital.

[18][22] The dubious safety of a bridge over the Ouse, a very short way north-west of South Lynn station, was allegedly a significant factor in the closure of the whole route,[22] and was demolished later that year.

A section of this line about half a mile (800 m) long[23] was left open for freight into the 1990s, transporting materials like oil and limestone to the sugar beet factory (since closed).

[30] The branch to the harbour was progressively shortened before its final closure at around the same time,[6] and the line to the docks closed as well (except for a short stub allowing the aforementioned freight trains from Middleton to change direction), the last train passing over the line in June 1994.

Before electrification in 1992, InterCity (and, later, Network SouthEast) diesel locomotives such as the Class 37[32] operated most services.

A new siding alongside the Middleton Towers branch line, which extends for 14 chains (920 ft; 280 m), was commissioned in August 2020, to enable 8-car electric multiple units to be stabled when not in use.

[35][36] The only freight activity around King's Lynn today is the sand trains which run from the Middleton Towers branch to either Goole, Barnsley or Doncaster.

In the past, through-trains from London always started from Liverpool Street, but services were shifted to King's Cross in the 1990s.

Before the May 2023 timetable change, Greater Anglia also operated a limited number a services to London Liverpool Street, which have since been withdrawn.

Restoration work began in April 2013 as a station rewire which quickly grew into a heritage inspired project.

The view taken was to restore the station to a 1949 state with British Rail branding and reminisces of the GER and LNER railways.

The project's completion was marked with Michael Portillo unveiling a plaque in the booking hall area on 22 July 2014.