The station is owned by VicTrack, a state government agency, and is operated by Metro Trains Melbourne.

[9][10] Glen Waverley station opened on 5 May 1930, when the railway line was extended from Eastmalvern.

[13] On 23 June 1979, a fire destroyed Tait motor carriage 339M whilst stabled in No.

The upgrade included a brand new station entrance, accessibility improvements and a new kiosk.

[19] In 2018, the station was chosen to be one of the stops on the under-construction Suburban Rail Loop East.

Early works on the project have already commenced in the suburb, with the line expect to open between Southland and Box Hill by 2035.

[20][21] The station is currently served by citybound services on the Glen Waverley line, which is operated by Metro Trains Melbourne.