The station is managed by ScotRail and is on the Fife Circle Line, 22+1⁄2 miles (36.2 km) north of Edinburgh Waverley.

This though followed a more southerly course through the town than the present alignment, which was built & commissioned by the North British Railway in June 1890 as part of the programme of works associated with the new Forth Rail Bridge.

The station was not listed for closure in the 1963 Beeching Report, but it lost many of its services in the years that followed - trains to the coast were withdrawn beyond Cardenden in October 1969, whilst the Kinross and Perth line was closed to all traffic just a few months later (on 5 January 1970) leaving only the route to Dunfermline & Edinburgh in operation.

Cowdenbeath thereafter became the terminus for most trains, with only a limited number of peak period services continuing through to Cardenden.

[3] Although some services now terminate at Cowdenbeath then return on the Edinburgh-bound track after reversing at the points located 13 chains (860 ft; 260 m) south of the station.