Inverurie was served by the Great North of Scotland Railway from its opening in 1854. Originally named "Inverury" - the contemporary spelling of the town name - the station was resited some distance to the east in 1902. This was a result of the railway constructing a new locomotive works at Inverurie (to replace the cramped Kittybrewster works) and the station was moved to an adjacent site.

Inverurie was also the junction for the Inverurie & Oldmeldrum Railway, which ran parallel to the mainline for some distance. When the station at Inverurie was resited, this made the branch line slightly shorter in distance.

The Inverurie & Oldmeldrum Railway was not very successful and closed to passengers in 1931 with the freight service surviving until 3 January 1966. The Locomotive Works at Inverurie, opened in 1902, were closed in the late sixties as a result of the closure of the lines they served. British Rail applied to the Minister of Transport for permission to close Inverurie Station (alongwith all stations on the ex-GNSR line to Keith Junction, with the exception of Keith itself), but Inverurie was one of only two examples where permission was not given (Huntly being the other example). Today Inverurie Station survives in use, although the buildings on platform 2 have been demolished. The platform edges for the Oldmeldrum Branch survive on platform 2, although the trackbed is now in use as part of a garden centre.

Inverurie Goods Yard remains in use by Engish Welsh & Scottish Railways (EWS), as does the GNSR-designed signalbox which was recently restored.