With the opening of the Seaton & Beer Railway on 16 March 1868 the name was changed to "Colyton Junction", before finally becoming "Seaton Junction" on 18 July 1869.
Originally, trains arriving from the Seaton branch had to reverse into the "down" (westbound) platform. However, when the station was reconstructed in 1927–8 with two through tracks on the main line and loops to the newly extended platforms, a branch line platform was added. This was set at an angle of 45° to the main line.
The location of the station created a major problem for westbound trains stopping at Seaton Junction since it was situated at the start of a six-mile climb at 1 in 80 to the summit of the line at Honiton tunnel.
The steady decline in holiday traffic resulting from increased car ownership in the 1960s led to a gradual run down of services and the branch line and junction station were closed on 7 March 1966 by the Western Region of British Railways.
The station building is now[when?] a private residence. The platform is still visible (albeit overgrown). The footbridge from the island platform still survives today.[when?]
Trains still pass the site on the West of England Main Line.
^Clinker, C.R. (October 1978). Clinker's Register of Closed Passenger Stations and Goods Depots in England, Scotland and Wales 1830-1977. Bristol: Avon-AngliA Publications & Services. p. 121. ISBN0-905466-19-5.
^"District Intelligence". Taunton Courier, and Western Advertiser. England. 14 May 1879. Retrieved 16 July 2021 – via British Newspaper Archive.
^"Presentation". Exeter and Plymouth Gazette Daily Telegraphs. England. 21 November 1882. Retrieved 16 July 2021 – via British Newspaper Archive.