The station opened as ’Crossharbour’ on 31 August 1987 but was renamed in 1994 to ’Crossharbour and London Arena’. After the neighbouring London Arena was demolished in 2006, the original name was reinstated. Just to the north of the current station, the London and Blackwall Railway built Millwall Docks station. This operated between 1871 and 1926.
The ’cross harbour’ name refers to the nearby Glengall Bridge across Millwall Inner Dock. The bridge’s construction was a neccessity for the developers to obtain planning approval for the dock when it was built in 1868.
In 1969 Tower Hamlets council completed the St John’s estate on the Cubitt Town side of the station. The project was begun 17 years earlier by Poplar Borough Council.