Following de-nationalisation of British Rail on 1 April 1994 the infrastructure to St Johns 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.

On 22 November 1999 Deputy Prime Minister John Prescott opened the 4·2 km Lewisham extension of London's Docklands Light Railway with trains running through to Bank.

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.

On 27 June 2003 the Strategic Rail Authority decided to strip Connex of the franchise citing poor financial management and run the franchise itself.
Connex South Eastern continued to operate the franchise until 8 November 2003 with the services transferring to the Strategic Rail Authority's South Eastern Trains subsidiary the following day.

On 30 November 2005 the Department for Transport awarded Govia the Integrated Kent franchise.
The services operated by South Eastern Trains transferred to Southeastern on 1 April 2006.

The loop line to St Johns was doubled in 2013.

There was formerly a bus terminus within the station, but this was relocated to Thurston Road as part of the Lewisham Gateway project.
Following de-nationalisation of British Rail on 1 April 1994 the infrastructure to St Johns 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.
On 22 November 1999 Deputy Prime Minister John Prescott opened the 4·2 km Lewisham extension of London's Docklands Light Railway with trains running through to Bank.
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.
On 27 June 2003 the Strategic Rail Authority decided to strip Connex of the franchise citing poor financial management and run the franchise itself. Connex South Eastern continued to operate the franchise until 8 November 2003 with the services transferring to the Strategic Rail Authority's South Eastern Trains subsidiary the following day.
On 30 November 2005 the Department for Transport awarded Govia the Integrated Kent franchise. The services operated by South Eastern Trains transferred to Southeastern on 1 April 2006.
The loop line to St Johns was doubled in 2013.
There was formerly a bus terminus within the station, but this was relocated to Thurston Road as part of the Lewisham Gateway project.
Lewisham station