The station was then closed between 1995 and 1998 due to repair work on the Thames Tunnel and from 22 December 2007 to 27 April 2010 for the extension of the East London line.

The present surface building is located a short distance to the south of the original entrance shaft to the Thames Tunnel.

The building was heavily refurbished for the re-opening of the ELL, with the entrance being enlarged by replacing two of the windows with arches.

The station's future was in doubt for a while after the announcement of the East London line extension, as Rotherhithe's platforms can only take four-car trains and cannot be lengthened.

A better view of the Thames Tunnel portals can be seen from the platforms at Wapping railway station on the opposite side of the river.