The station opened in 1849, serving the North Kent Line from London to Gillingham. The station building was rebuilt in 1906 in a London brick form typical of southeast London. It was again rebuilt in 1992-93 to a modern design in steel and glass by the Architecture and Design Group of British Rail, under the leadership of Nick Derbyshire. It has a, clean, naturally-lit ellipsoid theme, contrasting with the earlier forms. In 1973 a government report on the redevelopment of London's Docklands projected a greater form of the never-built "Fleet line" from Charing Cross via Fenchurch Street to Woolwich Arsenal and on towards Thamesmead, with a preceding stop at Silvertown. The Fleet line plans were shelved in favour of a route that became the western part of the Jubilee line. Council -approved however in 1980, finances meant that the Fleet line was never built. By the start of the 1990s plans emerged in both levels of government and business forums for the Jubilee Line Extension to serve the south bank of the Thames twice on its way to Stratford. In the Royal Borough of Greenwich the line takes in a small area, North Greenwich. Woolwich Arsenal was expanded in 2009, when Transport for London completed the construction of an extension of what was then termed the London City Airport branch of the Docklands Light Railway from King George V to Woolwich Arsenal. The official opening took place on 12 January 2009. In 2014, a petition was started and presented to the Mayor of London, Boris Johnson, to rezone Woolwich Arsenal station from Zone 4 to Zone 3. However he ruled this out, stating it would cause losses of over a million pounds a year.
The National Rail part of the station consists of two above-ground platforms. The up platform for London has a refreshment facility. The down platform serves trains going east, towards north Kent, via Plumstead, Abbey Wood and Slade Green. The Docklands Light Railway part of the station is underground, and consists of two platforms in an island platform configuration. As Woolwich Arsenal is a terminus, both platforms serve an up line to Bank or Stratford International via London City Airport and Canning Town. Trains depart in the eastbound direction due to the curve under the River Thames.
A Crossrail station is to be opened in north-east Woolwich, after a campaign to complement housing developments on public sector land. Among the successful lobbyists for this extra station were those who developed the land, including Berkeley Homes. It will be about 200m north of the main station on the north side of the A206 road.