The original plans for the DLR to Stratford included an option for a station at Pudding Mill Lane, to be called Stratford South. Funding was not available to build the station, but the location was one of two places safeguarded for future development, the other being Langdon Park.

The name of the station is taken from the nearby Pudding Mill Lane which, in turn, takes its name from the former Pudding Mill River, a minor tributary of the River Lea. This is believed to have taken its name from St. Thomas's Mill, a local water mill shaped like a pudding and commonly known as Pudding Mill. The area had also been called Knob Hill up until the 1890s.

The station opened in January 1996. It is next to the Olympic Park; however, it was closed for the duration of the 2012 Olympic Games and reopened on 12 September 2012. The original island platform station was permanently closed on 18 April 2014 in order to allow for the construction of a ramp from the new Crossrail tunnel portal nearby.

A new, larger station built a short distance to the south opened on 28 April 2014. The abandoned Pudding Mill Lane station was earmarked for quick demolition.