It was part of the Thameslink project that re-opened the Snow Hill Tunnel to provide a continuous north–south route across London.

Originally named St. Paul's Thameslink, it was renamed City Thameslink the following year to avoid confusion with the nearby St Paul's tube station on the Central line (note that out-of-station interchange discount does not apply for changing between these two stations).

[6] It is in Travelcard Zone 1 and one of the "core stations" on the Thameslink route, along with St Pancras, Farringdon and Blackfriars.

[9][10] The Thameslink line opened in 1988 after the Snow Hill tunnel, closed to passengers since 1916, was re-opened to provide a through route to Farringdon and King's Cross from South London.

[13] The new service was an immediate financial success, and it was decided to redevelop the Holborn Viaduct site with a new station and business complex.

[15][14] Because of a proposed routing for the second phase of the Jubilee line through the area, part of the station was built to allow for a future interchange.

New lighting, ticket gates and CCTV cameras were installed, and the service announcement system was upgraded to provide more accurate train times.

[20] In a 2014 report, London TravelWatch suggested an underground passageway linking City Thameslink to St Paul's tube station to provide an interchange with the Central line that would benefit passengers travelling from the Central line catchment to Gatwick and Luton Airports.

[28] The following January, several evening services from City Thameslink to St Albans and Harpenden were reinstated, after a six-month absence.