Ferntree Gully is a ground level premium station, featuring two side platforms.

[5] Like the suburb itself, the station was named after a fern tree gully that is located nearby in the Dandenong Ranges National Park.

[5] In 1963, flashing light signals were provided at the Alpine Street level crossing, located nearby in the down direction of the station.

[5] In 1977, the panel was abolished[5] and, in that year, boom barriers were provided at the Alpine Street level crossing.

[8] On 31 July 2017, with a budget of $20 million, work began to add 215 new parking spaces at the station, which was completed by 1 December of that year.