The original South Quay station opened in 1987, and was a standard DLR phase 1 elevated station, subsequently extended to permit the use of 2 car trains. The station was constrained by sharp curves at both ends and could not therefore be further extended on its former site. The DLR's plans to operate 3 car trains on this line therefore included the relocation of this station some distance to the east.
In 1996, near the station, the Docklands bombing killed 2 people and injured over 30.
In October 2004, Transport for London announced plans to close and replace South Quay station with a station at a new location because of increased use of the Docklands Light Railway. The reason for the move is that the platforms could only accommodate two car trains. They would need to be lengthened by thirty metres for three car trains but the curves either side of the station precluded extension work.
The new station, on a straight section of track 125m to the east, opened on Monday 26 October 2009 with the old station closing on Friday 23 October. A memorial plaque at the station was unveiled in December, commemorating the victims of the 1996 bombing.