[4][5] Initially opened as Lillydale, spelling that matched the original township, the station was given its current name of Lilydale on the 15 May 1888.

Lilydale station opened on 1 December 1882 as an extension of the railway line from Camberwell, which had been extended from Hawthorn in April of that year.

[6] When the new elevated station was constructed during level crossing elimination works between 2020–2022, the old ground-level building was retained.

The track from Lilydale to Yarra Glen, including Coldstream and Yering, is being repurposed as a rail trail.

[5] In 1985, boom barriers replaced hand gates at the former Maroondah Highway level crossing, which was located at the up end of the station.

[11][12] It crashed through a wire fence and traversed the Beresford and Nelson Roads level crossings,[11][12] and was about to climb a hill when it rolled back 300 metres.

[15] The rail bridge on John Street was demolished, and the land between it and the level crossing became an activity zone located underneath the new station.

[20] Platform 1: Platform 2: Martyrs Bus Service operates one route via Lilydale station, under contract to Public Transport Victoria: McKenzie's Tourist Services operates three bus routes via Lilydale station, under contract to Public Transport Victoria: Ventura Bus Lines operates six routes via Lilydale station, under contract to Public Transport Victoria: Mee's Bus Lines operates a V/Line coach service from Mansfield to Melbourne via Lilydale station.