[7][8] Mordialloc station was officially opened on 19 December 1881 by Sir Thomas Bent,[9] who was the Minister of Railways, and later becoming the Premier of Victoria between 1904 and 1909.

[11][12] The first train to arrive at Mordialloc was a special service from Princes Bridge, which collected school children from the Brighton area.

[9] On 31 July of that year, the line was extended to Frankston, and again was opened by Sir Thomas Bent.

By December of that year, through services were operating between the city and Mordialloc/Frankston, with the station itself open for goods traffic.

In December of that year, the Locomotive Branch of the Victorian Railways recommended the construction of an engine shed, at an estimated cost of £200.

[9] In 1887, an additional siding was provided, and occurring in that year, a contract was let for extensions to the station building.

By May of that year, the coal stage was relocated to Flinders Street and, by March 1889, a carriage dock was abolished, to allow an extension of the platform.

[4] The Staff and Ticket, which worked between Mentone and Mordialloc, was abolished, and the Winters Block system was provided, with the section remaining Mentone–Mordialloc.

Regrading occurred at the Up end of the station, with a railway overpass built over Nepean Road.

[9] In December that year, the Commissioners of the Victorian Railways inspected the station, and announced a proposal to replace the existing frame with a signal box at the McDonald Street level crossing.

[9] In 1910, duplication of the line between Mordialloc and Frankston occurred,[4] resulting in a rebuilt and enlarged yard and a complete overhaul to the station layout: a portion of a floating goods platform from Williamstown was erected by August 1 of that year, with instructions to reduce the length of the platform to 466 ft (142 m) also occurring.

[9] On 5 January 1911, a new, elevated signal box was provided adjacent to the Bear Street level crossing, complete with a fifty lever frame.

The Victorian Railways' Chief Engineer of the Way & Works branch recommended it be relocated to Colac, but it is unsure if this happened.

During November 1929, a number of roads in the yard were wired, allowing the use of electric locomotives on goods services.

[13] On 28 December 1938, the grandstand of the nearby Epsom Racecourse was destroyed by fire,[14] bringing an end to race traffic to Mordialloc.

During 1967, there was consideration to extending Platform 2 to allow 8–car trains, which would've forced the relocation of a number of signal posts.

[19][20] On 9 September 2013, whilst travelling through the McDonald Street level crossing, a wagon on the Long Island steel train derailed, causing lengthy delays.

[27] The designs for the new station was announced in June 2024 and will be elevated and the station to feature an island platform, the plans also show that the heritage building on Platform 2 to be kept and Bear Street to be closed off as part of the level crossing removal and McDonald Street to remain.

Platform 1: Platform 2: Kinetic Melbourne operates one SmartBus route via Mordialloc station, under contract to Public Transport Victoria: Ventura Bus Lines operates four routes via Mordialloc station, under contract to Public Transport Victoria: SkyBus also operates a service to Melbourne Airport via Mordialloc station.