In a statement the train operator said passenger numbers have doubled in the past two decades and Network Rail needs additional time to carry out essential maintenance and improvement work to give passengers at busier times of the day a better journey across the congested Southern network.
From Sunday (May 21), to coincide with the launch of the new timetable, there will be a key change to overnight train services from London Victoria and return.
Southern trains departing after 00.05 and before 04.52 from London Victoria and return will not run on Sunday to Thursday nights when passenger numbers are lowest.
Passengers with Southern tickets will be able to use Thameslink services from London Blackfriars or St Pancras International to travel between central London, East Croydon and Gatwick Airport/Brighton.
Late evening and overnight Thameslink services will call additionally at Purley, Coulsdon South, Merstham, Redhill and Horley as appropriate with some trains also running further than normal, to Haywards Heath and Brighton, to provide an alternative to Southern trains that will not run.
The Southern night service will be retained on Friday and Saturday nights when there is most demand.
The current arrangements, whereby Gatwick Express has no overnight services between 23:30 and 05:00, will continue.
Southern said: “The initiative will give Network Rail more time to carry out essential maintenance and improvement work overnight on the very congested Brighton Main Line, one of the UK’s busiest rail networks.
“It will also help Network Rail deliver critical elements of a £300m improvement plan that was announced by the Government in January.
“Ultimately it will help provide a more reliable and punctual train service and reduce delays for more than 300,000 commuters each day on the Southern network.”
Passengers are advised to check train times and station stops before they travel.