As part of the £5.5bn Thameslink Programme, Blackfriars Station is being redeveloped by Network Rail. The Thameslink Programme is designed to tackle the overcrowding on some of London's busiest rail routes, and to cope with the predicted growth in commuters in the future by increasing passenger capacity north-south to and through London. By extending the Thameslink line, it will help ease congestion in London bottlenecks as well as providing benefits to the passengers and to the environment.

Blackfriars Station is being redeveloped in order to manage the introduction of 12 car trains which will be more frequent, at up to 24 trains per hour, three times the current number of trains. In order to accommodate the extra services running on the line, the track is being realigned, which will remove the current bottleneck and will allow terminating trains to end on the west side of the station, whilst the through platforms will pass through the east side. This will mean that the trains will no longer have to cross lines, which is a major cause of delays at the station at present. The existing platforms will be extended and be covered by a new roof, making it the first platform to cover the entire length of a bridge over the Thames.

In order to accommodate the extended platforms, the existing bridge deck will be strengthened and widened on the west side. The extended bridge will be supported on one set of the existing disused piers that supported the former railway bridge, which will be strengthened and integrated with the existing pier to cope with the additional weight. Tony Gee has been appointed by Network Rail to prepare the detailed design of the bridge superstructure, substructure and foundations up to platform level.

The Station Building itself is being rebuilt to match the height of the existing station building and will have a façade primarily composed of glass. Inside the new building there will be a new shared ticket hall with National Rail and London Underground Limited (LUL) with new LUL ventilation shaft and escalators for access to the mezzanine (for National Rail services) and the sub-surface level (for the central/district LUL lines). There will also be a new South Bank station entrance, which will provide new access to the Tate Modern, the Globe Theatre and to the surrounding area.

The refurbishment works are due to start in 2009 and to be completed by 2011.