The station was closed in 1938 in advance of the relocation of Aldgate East to within minimal distance, rendering St. Mary's inessential.

In 1938, Aldgate East was relocated further eastwards and given a new entrance only a few hundred yards from St. Mary's (Whitechapel Road) rendering the latter surplus to requirements.

[2] During the Second World War, the station site was leased from London Transport by the Metropolitan Borough of Stepney for use as an air-raid shelter.

The structure was subsequently demolished, hence little evidence of the station's existence now remains above ground, and its site is occupied by a car dealership.

Loading gauge restrictions for the stock meant that, although the curve was double tracked, trains could only pass in one direction at any one time.