Nearby Penallta Junction gave access to the Great Western Railway and the Aberdare Valley, opened 1 April 1871 and the Cylla branch opened on 1 August 1906 to access the new Powell Duffryn owned Penallta Colliery.

The latter line closed in 1991 and has since been lifted, but the former is still in use (for freight only) as far as Cwmbargoed to serve the coal washery and associated opencast mine at Ffos-Y-Fran.

In 2014, the station underwent a £1.6 million refurbishment with new ticket machines, waiting areas and ticket office, with disabled toilet being installed in addition to major work carried out on the footbridge with lifts being installed to improve accessibility.

The northbound platform is signalled for use in both directions, to permit trains from Cardiff to terminate & start back from there.

Ystrad Mynach railway station was used as a location in the pilot episode of Porridge (Prisoner and Escort), part of the series Seven of One, starring Ronnie Barker.