The station, which was opened by the South Eastern Railway in 1890, is named after the nearby residence of the Cator Family, demolished in 1896.

Clock House retains its original street level booking hall and the remnants of its platform canopies and was formerly known for its tendency to flood whenever overwhelmed by the Chaffinch brook.

For example, the previous station signage used the latter (historically inaccurate) form, whilst the published timetables use the former version.

In connection with the electrification the track bed in the Clock House area was raised in an effort to reduce flooding.

[5] After World War II and following nationalisation on 1 January 1948, the station fell under the auspices of British Railways Southern Region.

[7] Following privatisation of British Rail on 1 April 1994 the infrastructure at New Beckenham station became the responsibility of Railtrack whilst a business unit operated the train services.

On 13 October 1996 operation of the passenger services passed to Connex South Eastern who were originally due to run the franchise until 2011.

Following a number of accidents and financial issues Railtrack plc was sold to Network Rail on 3 October 2002 who became responsible for the infrastructure.