The station's name matches that of the locality on which the suburb was built. Elizabeth Hopper was a gatekeeper, closing and re-opening a set of large timber level crossing gates whenever a train passed through. She and her husband, Stephen Hopper (1832-1908), a railway ganger, lived nearby with their eleven children.[6]
The original station was located on the down (Werribee) side of the former Old Geelong Road level crossing. Problems with stationary trains blocking the level crossing[7] led to the station being relocated to the up (Flinders Street) side of the crossing in July 1983, in conjunction with the electrification of the line to Werribee.[4] Also in that year, boom barriers were provided at the former level crossing.[4]
On 4 May 2010, as part of the 2010/2011 State Budget, $83.7 million was allocated to upgrade Hoppers Crossing to a premium station, along with nineteen others.[8][9] However, in March 2011, this was scrapped by the Baillieu Government.[10]
The crossing was removed as part of the Level Crossing Removal Project,[11] and was replaced with a road overpass 800m to the east of the crossing, directly connecting Old Geelong Road with the Princes Highway. Construction began in February 2021 and,[12] on 9 December of that year, the new road bridge opened to traffic.[13] The level crossing was closed to road traffic on the same day,[13] and was replaced with a pedestrian overpass, which opened in February 2022.[14]