On 21 December 2004, City One station opened to the public with the rest of KCR Ma On Shan Rail stations.
On 14 February 2020, the Ma On Shan line was extended south to a new terminus in Kai Tak, as part of the first phase of the Shatin to Central Link Project. The Ma On Shan Line was renamed Tuen Ma Line Phase 1 at the time. City One station became an intermediate station on this temporary new line.
On 27 June 2021, the Tuen Ma line Phase 1 officially merged with the West Rail line in East Kowloon to form the new Tuen Ma line, as part of the Shatin to Central link project. Hence, City One was included in the project and is now an intermediate station on the Tuen Ma line, Hong Kong's longest railway line.