The station was opened by the Metropolitan District Railway (MDR, now the District Line) on 3 June 1889 on an extension from Putney Bridge station to Wimbledon. The extension was built by the London and South Western Railway (L&SWR) which, starting on 1 July 1889, ran its own trains over the line via an eastward-facing loop that joins the Clapham Junction to Barnes mainline.

The section of the District Line from Putney Bridge to Wimbledon was the last part of the line to be converted from steam operation to electric. Electric trains began running on 27 August 1905.

Mainline services through East Putney were ended by the Southern Railway (successor to the L&SWR) on 4 May 1941, although the line remained in British Rail ownership until 1 April 1994 when it was sold to London Underground for the nominal sum of £1. Until the sale, the station was branded as a British Rail station.