The station was built by the Taff Vale Railway (TVR) and opened on 9 October 1840.

[2] It was progressively remodelled during the 19th century, but its present appearance derives largely from reconstruction carried out between 1907 and 1914.

Reflecting both the narrow steep sided topography of the valley, and the need to accommodate many converging passenger routes and passing coal trains, it is effectively designed as two back-to-back termini.

Architecturally, the 1912 station still includes all the original red brick and terracotta buildings on the island platform, some of which remain in public use, e.g. as ticket office and waiting room.

The elaborate 1912 main station façade in the same art nouveau style was destroyed during modernisation in the mid 1970s and replaced by a featureless red brick wall.

Passenger services, which used the TVR's station at Pontypridd, began on 28 December 1887, and were operated by the Alexandra (Newport and South Wales) Docks and Railway (ADR), which absorbed the PC&NR in 1897.

With the Beeching Plan reducing passenger traffic (the line to Aberdare closing in March 1964), and falling coal production, track simplification was carried out by British Rail in 1974, resulting in the removal of all track from the eastern side of the island platform.

However, with the subsequent re-opening of Aberdare and the growth of passenger traffic, British Rail added a new northbound platform in 1990–1991.

As part of a £200m regeneration scheme to boost train capacity in Cardiff and the surrounding areas, Pontypridd received a third platform in December 2014.

[8] Work began in 2014 to build this platform in the station, to accommodate more trains and to increase the number of services to Cardiff.

[9] During Monday-Saturday daytimes, there are usually six trains an hour from Cardiff Central, made up of a half-hourly service frequency on each of the three branches, i.e. to Treherbert, Merthyr Tydfil and Aberdare.

A reduced service operates on Sundays, with two-hourly frequencies on all three northbound routes and three trains every two hours southbound to Cardiff and beyond.

The service from this station towards Porth and Treherbert was suspended in summer 2023, due to major route upgrade work being carried out at multiple locations as part of the Valley Lines electrification scheme.

Some evening trains on the Aberdare and Merthyr branches were also replaced by buses during this period as part of the same work.