It serves as an interchange between the Airport, Armadale, Ellenbrook, Fremantle, Midland, and Thornlie lines as well as Transwa's Australind service.

[10] Starting in 1988 the station underwent a major upgrade as part of the Northern Suburbs Transit System project, which included the construction of a new island platform, a steel and glass roof that covered the central platforms, an adjoining multi-storey car park, and the Citiplace Centre retail and community services hub built on a level above the existing station platforms which also connected pedestrian footbridges linking the Perth Cultural Centre and the Forrest Chase shopping complex to the station.

[11] With the introduction of the SmartRider contactless electronic ticketing system and installation of fare gates, Perth railway station became a closed station in early 2007;[12] as a result the entrance on the Horseshoe Bridge was fenced off and its wooden stairway and overpass was later removed.

[14][15] Further changes to the station occurred as part of the Perth City Link project in the early-2010s, which saw the above ground rail lines west of the Horseshoe Bridge sunk and the existing platforms and overpass there demolished to make way for a new public space, Yagan Square.

The station also saw the construction of a new pedestrian underpass connecting the three main above ground platforms, and upgrades and extensions to the roof.

As of August 2023, Wellington Street has been upgraded to include eleven bus stands outside the station, seven eastbound and four westbound.