Westall station originally comprised two workers-only platforms for staff at the adjacent Martin & King railway coach-building factory. The station became available to the general public on 1 June 1959, and all trains began stopping there.
The station had a stabling yard located at its southern end, as well as a number of industrial sidings serving nearby factories. On 17 April 1998, the Westall train maintenance centre was officially opened in the former goods yard, as part of the decentralisation of train stabling and maintenance from the former Jolimont Yards. The buildings were approximately 2,850 m2 in size, and permit bogie repair and replacement, under carriage and overhead work. The facility cost $15 million, which also included the Bayswater facility.
The former Westall Road level crossing, which was located at the Down end of the station, was replaced with an overpass in 2000.
On 26 July 2006, a fire in the waiting room on Platform 1 caused major damage to half the station building, the ticket machines, seats, and a section of the platform. The city-bound platform was closed off and passenger services to Flinders Street ran express from Springvale to Clayton, bypassing Westall, until temporary fencing was placed around the building. The damaged section was subsequently demolished and rebuilt.
In May 2008, the Victorian state government announced that the Westall station precinct would receive a $151 million upgrade, which included a rebuilt station, a new third platform, a third 2.6-kilometre track between Centre Road and Springvale Road, and additional storage space at the Westall stabling yard. Work commenced in January 2010, with the majority of the works completed by October of that year. Following these works, Westall was upgraded to a Premium Station.