The original idea for a railway line serving Mortlake was first tabled in the 1870s. The line had been completed, but not used until 1889, when the Mortlake Despatch ran a newspaper article questioning why the line was not yet in operation. The line was officially opened on 4 February 1890. Soon after, additional facilities were provided, such as a windmill, 10 ton weighbridge and stockyards. The Koonendah Railway Station Post Office opened on 1 December 1890 but closed in 1891.
The line was closed to all traffic on Tuesday, 1 August 1978. Dismantling of the line occurred during May/June 1988.