One of the most interesting stations in the London area was constructed on the south side of the hill on which the Crystal Palace was re-erected, following its siting in Hyde Park in 1851 for the Great Exhibition.

In order to bring the large crowds attracted to the site, eventually two stations were built - one slightly higher up the hill than the other. High level was a large and spacious terminus on a branch of the South Eastern Railway closed in 1954. Low Level started as a London, Brighton & South Coast Railway terminus in 1854. It stood at the end of a short spur from the London Bridge to Croydon line, but soon became partly a through station when connected to the west of London by the West End and Crystal Palace Railway in 1856.

A third line connected it southward to Norwood junction in 1858. In 1857, an eastward connection was made to Norwood Junction (for the Brighton line to the south) and in 1858 the WEL&CPR was extended as far as Beckenham. From 1860 direct services were available from London Victoria.

From the outset trains were operated by the London, Brighton and South Coast Railway (LBSCR). Initially the station was the terminus of a spur line from Sydenham. In 1856 the station was able to take through train services to Clapham Junction via West Norwood and Streatham Hill, following the completion of the 746 yard (690 m) Crystal Palace Tunnel. Although relatively short, the tunnel was regarded as a major engineering achievement as it was cut "through the same treacherous material [clay], through the hill on which the Crystal Palace stands, and immediately under one of the great water towers, a superincumbent weight of 2,200 tons which taxed in its execution all the skill and workmanship of the eminent contractors."

The frontage of the station was rebuilt in 1875, and was described: "Although the Roman Catholic chapel room is no longer used the station still has a cathedral-like atmosphere as one passes from the period booking hall to the vault-like station and the stairs down to the original station area"

The description relates to the trainshed roof above the staircases at the west end. However, the rest of the station has no shelter from the elements between the vast brick retaining walls. Originally the whole length of the platforms beyond the bottom of the massive staircases was covered by an elegant dual bow-spring arch iron roof. This was removed as a precautionary measure shortly after the collapse of the similar structure at Charing Cross in 1905.

The line was electrified between Balham and Crystal Palace on 12 May 1911, using the LBSCR overhead system, in time for the Festival of Empire coinciding with the coronation of King George V. Electric trains from Victoria were advertised to complete the journey in fifteen minutes - a running time that has never been equalled.

The station is built on the junction of two lines: the old station platforms lying on the Sydenham route, and the more modest platforms on the southern spur to Beckenham Junction.

After World War II when the Palace itself no longer existed as a major attraction, there was a move of most services through the station to serve London-Croydon routes rather than running along the outer South London Line. The southern platforms became the busier pair and the entrance to the station was moved to the south side of the building in the 1980s. The glazed ticket hall was constructed at this time, which echoes the profile the Crystal Palace with its arched roof structure.

The original station was partially refurbished in 2002 by Railtrack at a cost of £4 million. This included a substantial amount of work on the roof of the building and refurbishment of office space on the top floor.

The two outer bay platforms, which were used for trains terminating there, are no longer in use, although the track and buffers are extant (The third rail has been removed). When the East London Line extension is constructed this will terminate in one of the bay platforms and a new island platform, replacing the removed sidings in the centre of the old station. By 1970 it was expected that the residual traffic at Low Level would not justify its continuation as a station and an alternative use was being considered. This coincided with the debate as to the future of the National Transport Museum at Clapham. This was on land owned by British Railways who were keen to realise its value.

There was strong political pressure from the then Minister for the Arts, Jennie Lee, to move the railway objects to York where there was already a railway museum, but the Transport Trust and others wanted them to remain in London as part of a museum for all land transport. A change of government opened an opportunity, and the Transport Trust pressed the new government to reconsider. Lord Eccles, Paymaster General responsible for the Arts, invited proposals for a comprehensive scheme on a site in the London area, with rail connection, room for all the Clapham exhibits and for expansion, and subject to the condition that the cost could be covered.

The Transport Trust in cooperation with the Clapham Society and Sir Robert McAlpine & Sons put forward a scheme estimated to cost £515,000 - while £500,000 would be realised from the sale of the Clapham site, a further £60,000 would be available for housing the British Transport Records to be moved from Paddington. The value of the site at Crystal Palace was estimated at £25,000, so the project more than covered its costs. There would have been six tracks for rail exhibits, while London Transport and other road vehicles would be accommodated on the first floor. There was a goods yard suitable for a turntable and the preservation of diesel and electric locomotives and one and a half miles of track suitable for steam trains. There was also space for a tram shed and track, and access to the Crystal Palace race track, where vintage vehicles could be run.

The scheme foundered as BR delayed closure of their lines and meanwhile London Transport were anxious to have an alternative to Clapham. In 1972 they looked to the Transport Trust to support their idea to use their power station at Greenwich which was converting to gas-turbine operation, leaving the Turbine Hall vacant. In the end the Trust suggested Syon Park, Chiswick for the LT collection and it was moved there. The availability of space at York ended the debate and so the idea of a national transport museum was lost, split between rail and LT.