In the 1850's Herne  Hill was still a very rural community, with a handful of large country houses surrounded by farms. In 1860 the London, Chatham and Dover Railway obtained the right to build two inner London lines: one from Beckenham Junction to Victoria via Herne Hill; and another, a 4.5 mile  extension known as the City Branch, from Herne Hill to Farringdon.

Herne Hill station and the first line section to be completed, from Victoria to Herne Hill via Stewarts Lane and Brixton, opened on 25 August 1862, so Herne Hill Station celebrates its 150th anniversary this year.

The station was designed by architect John Taylor and railway engineers Joseph Cubitt and J.T. Turner. As an important junction station the building was quite impressive; it had tea rooms offering buffets, decorative brickwork and a tower (which also served the practical function of concealing the water tank for steam locomotives). There were initially two platforms at the station:  Up was accessed from the upper floor of the station building via a stairway outside the building and down from an island platform. The station's original signal box, elevated above the railway viaduct at the junction between Norwood Road and Half Moon Lane, was a prominent feature in Herne Hill for many years.

On 6 October 1863, the City Branch opened from Herne Hill as far as Elephant & Castle, via Camberwell and Walworth Road (the platforms at Loughborough Junction, now the closest station to Herne Hill, opened in 1872) The line from Beckenham Junction reached Herne Hill from the south in July 1863 connecting the station to the LCDR's lines in Kent, By June 1864, the City Branch had been extended to Blackfriars Bridge railway station (on the south bank of the River Thames) via Borough Road.  Blackfriars Railway Bridge was then built across the Thames and a terminus for trains from the south opened at Ludgate Hill on 1 June 1865.  The opening of Snow Hill tunnel in January 1866, enabled trains from Herne Hill to reach Farringdon and complete the Metropolitan Extension. The junction was completed in 1868 when a spur was built to connect with the LBSCR line from London Bridge to Sutton at Tulse Hill.

The ease with which one could reach both the City and the West End, as well as the links to other parts of South London, resulted in much building in the area and the fairly rapid replacement of the large houses and farms with rows of terraced houses as well as some more superior houses to the east of the area, along Half Moon Lane, and the surrounding roads .
Up Mainline trains, from Dover  and Chatham were split at Herne Hill, giving easy access to the City and West End, and in the other direction were joined there, This gave good access to Cross Channel steamers, and was the most direct route to Paris and the rest of Europe.

Suburban services included trains to Hatfield in the north and Wimbeldon and Kingston in the south-west, as well as services to Beckenham and Bromley.

The LCDR enlarged the station in 1884 to meet growing demand and the viaduct was widened to allow for the construction of a second island platform and two lines to the east (the easternmost line was used only for freight; and the foot tunnel under the viaduct was opened. In 1885, the LCDR decided to use Blackfriars Bridge railway station solely as a goods yard but lacked the space to sort wagons at the site. It purchased 14 acres of land between Herne Hill and Loughborough Junction for this purpose. The Herne Hill Sorting Sidings had some 35 sidings, the longest of which was 940 ft  In 1899 the LCDR combined with the South Eastern Railway to form the South Eastern and Chatham Railway.  Services to Farringdon from Herne Hill were discontinued in 1916 with the closure of Snow Hill tunnel to passengers, and trains from the south terminated at Holborn Viaduct instead. Freight services continued until the 1950's.

The LCDR amalgamated with the LB&SCR, SER and several other railways to form the Southern Railway at the start of 1923. Electrification started in 1924 and was completed in 1925 to Orpington.  Herne Hill station was extensively remodelled as part of these works; the eastern island platform was lengthened; the original island platform was demolished and replaced by one further west (allowing two tracks to be laid between the island platforms); the western sidings were removed. The distinctive signal box overlooking Norwood Road and a similar signal box at the northern end of the station were demolished in 1956 and replaced by a single signal box adjacent to the north junction.

By 1959, the pattern of commuter services at Herne Hill had taken the shape it would hold into the 21st century: all-stop trains from Victoria to Orpington and from the City of London to Wimbledon and Sutton via West Croydon.

The Herne Hill Sorting Sidings closed on 1 August 1966 . Nothing of the sidings remains: residential accommodation has been built along Shakespeare Road (on the western sidings) and commercial premises have been built along Milkwood Road (on the eastern sidings).
In 1988, Snow Hill tunnel re-opened and the former LCDR City Branch formed the basis of the new Thameslink route.  There was a plan for Eurostar to come through Herne Hill on new trackage but this was plan was abandoned and although both a different route and London terminus for HS1 were eventually chosen (St Pancras via East London), Eurostar services linking London Waterloo to Brussels and Paris passed through Herne Hill without stopping from 1994 until the completion of HS1 in November 2007. This marked the end of rail services to the continent via Herne Hill, which had been started by the LCDR in 1863 when the line between Victoria and Dover via Herne Hill was completed.

The upper floor of the station, which had not been used by passengers since 1925, was converted into 3,000 sq ft of office space in 1991 and rented as 'Tower House' (after the station's distinctive tower). The disused freight line to the east of the station was partly reopened in 2009 as a siding for use by First Capital Connect trains to compensate for the loss of sidings when the Moorgate Thameslink branch was closed. The line's connection to the south junction was severed during these works. The station had become fully accessible by 2010: lifts were installed to provide step-free access to the platforms in 2008 and a unisex disabled-accessible toilet was opened on the southbound platforms in 2010.