Folkestone has operated a regular service to mainland Europe since 1843, with passengers arriving at the port by rail from London, via Reigate and Tonbridge. A temporary terminus near the site of the current station was used for six months until the Foord Viaduct - with its nineteen arches - was completed. 

The railway approaches the harbour at right angles, with a steep drop of 34 m (111 ft) over a distance of 1,214 m (1328 yds), leading to a level railway pier which bisects the harbour. In 1849 a swing bridge was constructed, permitting rail access to steamer berths on the harbour’s south side and operation of passenger boat trains.

The nineteen acre harbour had been constructed by Thomas Telford in 1809; when purchased by the South Eastern Railway it was heavily silted and required significant work to clear channels. The company was not permitted to operate their own vessels and chartered ships from the New Commercial Steam Packet Company. The first steamer arrived on 1 August 1843, the 190 tonnes vessel 'City of Boulogne'. Later that day saw the departure of the 'Sir William Wallace' carrying 75 passengers and the arrival of the 'Emerald' carrying 142 passengers.

The directors of the company soon formed the South Eastern and Continental Steam Packet Company and operated eight newly constructed steamers on their Folkestone ‘“ Boulogne and Dover to Ostend and Boulogne routes until 1853 when the railway company was granted parliamentary approval to operate its own vessels. In the first half of 1854, 31,594 passengers crossed from Folkestone to Boulogne; only 12,132 passengers took the Dover-Calais route. However, in 1861 the London, Chatham & Dover Railway reached Dover; in 1862 the South Eastern steamers were exclusively employed on the Folkestone ‘“ Boulogne crossing. In 1867 the direct rail line from Paris to Calais was extended to Boulogne; the marginally shorter Dover ‘“ Calais route progressively saw increased traffic.  

A new low water pier opened in 1861 permitted operation of larger steamers; although this was some distance from the Harbour Station, the original South Pier was still preferred for the majority of sailings. Increasing passenger numbers led to the extension of the railway lines towards the New Pier in 1876; when the pier was lengthened between 1881-83, services from the old South Pier effectively ended. In Boulogne the present deep water berths were constructed on the Quai Chanzy and the railway lines extended to the site of the Gare Maritime; for the first time, trains were able to pull-up alongside the steamers. Between 1897 and 1904, the New Pier was again extended and widened.

In 1899 the two railway companies merged to form the South Eastern & Chatham Railway, again permitting inter-operability at the two ports. The SE&CR was absorbed into the Southern Railway in 1923. The line was electrified in 1961.

Freight services on the branch line were withdrawn in 1968. The opening of the Channel Tunnel in 1994, leaving just two daily services from Folkestone; when these were transferred to Ramsgate, the station was closed to ordinary traffic in 2001 and the line singled. On 12 April 2008 the station was formally closed, although a steam hauled rail tour visited on 14 March 2009; six days later,  Network Rail announced they had begun the formal process to close the line and station on cost grounds, having redeveloped Folkestone West with new waiting facilities for the VSOE passengers. Current redevelopment plans for the harbour would see the demolition of the rail viaduct.