The station opened in 1990 to replace Holborn Viaduct railway station. 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. The station was refurbished in 2010–11 to increase capacity, and the timetable was revised in 2018 with the introduction of automatic signalling.