[9] Clayton station is currently served by the Pakenham and Cranbourne lines which are both part of the Melbourne railway network.

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

The length of the platform is approximately 160 metres (520 ft) long enough for a Metro Trains 7-car HCMT.

[16] In 1971, boom barriers replaced interlocked gates at the former Clayton Road level crossing, which was located at the up end of the station.

[20] In 2016, the Andrews government announced that, as part of the Level Crossing Removal Project (LXRP), 8.3 kilometres (5.2 mi) of elevated rail would be provided, removing nine level crossings on the Pakenham and Cranbourne rail corridor, including the building of five new elevated stations at Carnegie, Murrumbeena, Hughesdale, Noble Park and Clayton.

[21] Dubbed "sky rail" by opponents and some media outlets, the plans for an elevated railway spurred significant local opposition due to concerns over visual and noise impacts.

[9] The removals created a large new section of open parkland, dubbed a "linear park".

[26] This included 22.5 hectares (56 acres) of new open space, sports courts, playgrounds, new walking and cycling trails, and expanded station forecourts.

[27][28] As part of the project, the Djerring Trail was created, a 17-kilometre (11 mi) shared-use path along the rail corridor, which runs through the Clayton station precinct.

[8] Services to East Pakenham and Cranbourne travel together south-east towards Dandenong before splitting into two separate lines.