[2][3] The SER was at that time engaged in a bitter feud with the London, Chatham and Dover Railway (LCDR), which opened a station (adjacent to the church) named Lewisham Road as part of the initial section of the Greenwich Park branch line in 1871; this, coupled with the development of the area, may have been a factor in the building of the station.

The main line was electrified, with the (750 V DC third rail) system, in February 1926 for the operation of electric services to Cannon Street or Charing Cross to Orpington.

On 4 December 1957, two trains collided just south-east of the station on the main line bypassing Lewisham, bringing down the Lewisham-Nunhead railway bridge and killing 90 people.

[6] Following privatisation of British Rail on 1 April 1994, the infrastructure at St Johns station became the responsibility of Railtrack, while a business unit operated the train services.

On 13 October 1996, operation of passenger services passed to Connex South Eastern, which was 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, which became responsible for the infrastructure.

[4] As of 2017[update], the station was reached by a footbridge from St Johns Vale, there being no direct road access.

There was a signal box at the south end of the station; this closed and was demolished when the area was resignalled in the mid-1970s.