The Bill for the Lynn and Ely Railway received Royal Assent on 30 June 1845. Work started on the line in 1846 and the line and its stations were opened on 27 October 1846. Watlington station opened with the line and was, as it is now, situated South of Lynn station (now King's Lynn). The station to the south was St Germain's station. The line ran from Ely to Downham, the eventual destination being Ely.
Watlington station, from 1847 part of the East Anglian Railway, became part of the Great Eastern Railway in 1862, and was renamed Magdalen Road in 1875. From 1848 on wards, Watlington was a junction, as the line once branched off from there to Wisbech. The branch, along with Magdalen Road station, was closed in 1968.
Due to local efforts, however, Magdalen Road station was reopened in 1975, and in 1989 returned to its original title of Watlington. The signal box at the station, in active use today, still bears a Network SouthEast sign with its post-1875. The current southbound platform, behind the signal box, dates from the early 1990s; the original station buildings on the southbound side have since been converted into a private residence. The original wooden waiting room on the northbound platform was replaced around the same time, though the original platform still survives as part of an extended platform.
Before electrification, services were normally operated by InterCity locomotive-hauled trains, normally pulling British Rail Mark 2b coaches. The locomotives were usually Class 37 diesel-electrics, sometimes Class 31s or 47s. Off-peak links were often provided by Metro-Cammell diesel multiple units.
