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).

[28][29] The closure of these services left only one passenger route in operation—services to Ely and Cambridge on the Fen Line.

[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.

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change, Greater Anglia also operated a limited number a services to London Liverpool Street, which have since been withdrawn.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