Originally, Durham was served by three stations. Former Gilesgate Railway Station, Durham (now a hotel) was the first  and was built in 1844. It was at that time the main station for trains to London. It was the railway entrepreneur George Hudson who built the main line northwards from York from around 1841. Near Durham, his line was what is known as the Leamside line, and lies to the east of the city. Hudson's line was called the Newcastle and Durham Junction Railway and it became part of the North Eastern Railway in the early 1850s.

Gilesgate station was built in stone by the architect G.T. Andrews of York. It is an attractive single storey building with a Georgian station master's house adjacent. Although closed for passengers in 1857, it survived as a goods station until 1966. In 1857, the current Durham railway station and the viaduct immediately to the south were built as a terminus of a branch from Bishop Auckland.  In 1871 a new line was built from the existing main line at Tursdale to the new Durham station, then continued to Newcastle Central via Chester-le-Street. This soon became the main line.

The Leamside line declined in importance, and closed together with the Gilesgate branch. Passenger services to Newcastle via the Leamside route ended in 1963, whilst those to Bishop Auckland and Sunderland via Penshaw were withdrawn on 4 May 1964.

The current station, built in 1857, possibly by Thomas Prosser, is a handsome two storey house with castellated portico, all in a neo-Tudor style in dressed sandstone. The handsome iron canopy of 1872 on the down platform has been restored. From its platforms can be enjoyed one of the best views in England, of Durham Cathedral and castle.

A third station was built at the end of the Durham, Elvet & Murton  branch line in 1893. It was on the eastern side of the city, at the end of a street called Old Elvet. Elvet Railway Station was closed in 1931 and demolished in 1963 to make way for Magistrates' Courts. It was a single storey building with steep roof, a clock in a dormer with pointed roof, and had only two platforms.