A pair of dual gauge tracks for the South Kensington–West Footscray line run in a cutting under the station before entering the Bunbury Street tunnel,[7] providing a rail link to the Port of Melbourne and other freight terminals, as well as access to Southern Cross station for the NSW TrainLink XPT, The Overland, and V/Line Albury passenger services.

Quadruplication of the tracks towards Melbourne in November 1976 eliminated the switched junction and so the signal box was closed, although the building is listed on the Victorian Heritage Register.

On 31 May 1996, Footscray was upgraded to a premium station, although the enclosed waiting area and ticket facilities were built in 1993, as part of the "Travel Safe" program of the early 1990s.

[13] During the 2017/2018 financial year, Footscray was the sixth-busiest station on the Melbourne metropolitan network, with 5.26 million passenger movements recorded.

[14] From 2012 to 2014, Footscray station underwent a major upgrade and conservation works as part of the Regional Rail Link project.

They reopened when the new Regional Rail Link tracks between Sunshine and Southern Cross were brought into service on 16 July 2014.

[16] New canopies, stairs and escalators were installed at the Irving and Hyde Street ends of the footbridge, and wider ramps were built from the footbridge to the platforms and the street level, to allow easier access to the platforms.

Platform 3: Platform 4: Platform 5: Platform 6: CDC Melbourne operates six bus routes via Footscray station, under contract to Public Transport Victoria: Kinetic Melbourne operates three bus routes via Footscray station, under contract to Public Transport Victoria: Transit Systems Victoria operates five bus routes via Footscray station, under contract to Public Transport Victoria: Yarra Trams operate one route to and from Footscray station: Media related to Footscray railway station at Wikimedia Commons