In March 1884, the railway line was extended via Midland Junction to Bellevue[2][3] and later to Clackline, York and Northam.

A dedicated freight line was later added on the western side between Cottesloe and the Leighton Marshalling Yard.

[4] On 22 October 1898, the railway line was extended south to Robbs Jetty, on 1 July 1903 via Cockburn to Coogee and on 19 December 1955 via Woodman Point to Kwinana.

[3][7] In July 1926, the Fremantle Railway Bridge over the Swan River was partly washed away in a flood, with one line restored in October 1926 and the second in April 1928.

[4] In the 1960s, as part of the standard gauge project, the section south of Cockburn was replaced by the Kwinana line on a different alignment.

The closure of the line was opposed by Friends of the Railway (FOR), which submitted a petition of 100,000 signatures and prepared a 98-page report arguing for its retention.

[11] Later when a narrow gauge link was constructed from Cockburn to North Fremantle, trade unions had placed a ban on working on dismantling any track or equipment.

[12] The service was reinstated on 29 July 1983 following a change of government which saw Brian Burke and the Australian Labor Party (ALP) come to power.

The Hotham Valley Railway operated a daily service on this section of the line with a W class steam locomotive as the Spinnaker Run between October 1986 and February 1987.

[21] Between 2011 and 2014, the Fremantle line was sunk between Lake Street and the Horseshoe Bridge in the Perth CBD to allow for the redevelopment of the area.

[26] With the privatisation of Westrail in 2000, responsibility for the Perth to South Beach section passed to the Public Transport Authority and the South Beach to Cockburn Junction section to Arc Infrastructure, although operational responsibility for the standard gauge line is with Arc Infrastructure.

When the Airport line began operation,[43][44] weekday peak period frequency between Claremont and Fremantle was reduced to five trains per hour.