The station was opened as 'Highbridge' on 14 June 1841 when the Bristol and Exeter Railway opened its broad gauge line as far as Bridgwater. A road crossed the line at the north end of the platforms, and a goods shed was provided beyond this on the west side of the line. This company wasamalgamated with the Great Western Railway on 1 January 1876.
On 28 August 1854 the Somerset Central Railway was opened from Highbridge to Glastonbury. This later became the Somerset and Dorset Joint Railway, but it was worked by the Bristol and Exeter company and was also broad gauge for the first few years and a connection was provided between the two railways in the goods yard. A separate set of platforms were provided on this line which eventually had two terminus platforms and two platforms on a through line that led on to an extension toBurnham-on-Sea. To reach this the line crossed the Bristol & Exeter main line on the level just north of the road bridge. The Somerset & Dorset goods traffic was mainly handled at Highbridge Wharf which was on the Burnham-on-Sea branch.
Highbridge was not only an important station on the Somerset & Dorset: it was also the site of the company's locomotive works, which closed in 1930, and a small engine shed that remained open until the line and station finally shut in 1966.
Following the nationalisation of the railways, the Somerset & Dorset line platforms were shown in timetables from 26 September 1949 as 'Highbridge East', and the Bristol & Exeter line platforms were known as 'Highbridge West' from 5 May 1950. Regular through trains to Burnham ceased on 29 October 1951, though the line remained open for occasional summer special trains until 8 September 1962. Following this closure the station became 'Highbridge and Burnham-on-Sea' on 30 June 1962.
The remaining Somerset & Dorset line passenger services to Evercreech Junction were withdrawn on 7 March 1966 which left just the main line platforms, as had been the case before 1854. Milk trains continued to run on the Somerset & Dorset line as far as Bason Bridge and a new connection from the southbound main line was installed 4 April 1971 but the trains were withdrawn and the line closed on 2 October 1972; goods traffic at Highbridge itself had ceased on 2 November 1964.
On 6 May 1974 the 'and Burnham-on-Sea' was dropped and the station reverted to its original name of 'Highbridge', but became 'Highbridge and Burnham' on 17 May 1991.
The main entrance to the station is on the town (western) side of the line and this gives access to Bristol-bound platform. The Taunton-bound platform can be reached by the footbridge, or through the housing estate that occupies the site of the former Somerset & Dorset platforms. Both main line platforms extend south across the tidal River Brue.