1928–1956

On 16 October 1928, after the reinstatement of a passenger service on the Fawkner – Somerton line in March of that year, Rail Motor Stopping Place No. 21 opened at the site of the present Gowrie station.^[4] It was closed nn 5 May 1956, when the passenger service ceased.^[4]

1965–present

On 17 May 1965, Gowrie station opened in its current form, on what was by then the Upfield line.^[4][5] The name of the station derives from a former grazing property called Gowrie Park, which the owner named after Gowrie, in the UK.^[6][7][8] The Fawkner Crematorium and Memorial Park is located on part of the former property.^[6]

Just after 4:45am on 2 August 1977, a seven-car Harris train set rolled away from the station when the driver and guard were changing ends, having taken the train out of a siding, prior to operating a city-bound service from Upfield.^[9][10][11] The train passed through fifteen level crossings and destroyed seven sets of hand gates before stopping just after Brunswick, between the Albert and Dawson Streets level crossings.^[10][9][11]

In 1998, Gowrie was upgraded to a premium station.^[12] Also in that year, the track from Fawkner to Gowrie was duplicated and boom barriers were provided at the Box Forest Road level crossing, in the down direction from the station.^[13] Immediately north of the station, the double track merges into a single track, which continues to the terminus at Upfield.^[4] Prior to 1998, Platform 1 was a dock platform for terminating trains,^[14] which meant that trains could not pass each other there, but had to do so further down the line at Merlynston.

Under the 2013 PTV Network Development Plan, the line between Gowrie and Upfield was to be duplicated, and the line to Roxburgh Park reinstated. That was to include a flyover across the North East standard gauge line, to allow Seymour V/Line services to run via Upfield, and eventual electrification of the line to Wallan.^[15]