Commuters could be caught out by the alterations which will see many existing trains leaving stations up to two minutes early.
Bosses at parent company Govia Thameslink Railway claimed the revised schedule will create room for 40,000 extra passengers during rush hour.
The new weekday timetables, starting on May 21st, will also see a train every 2.5 minutes between Blackfriars and St Pancras.
Other improvements include direct services running from Cambridge to Brighton and from north Kent to Luton.
We are redeploying trains and crew and there may be some disruption, so we ask passengers for their understanding during the transition period of several weeks during which time a very small number of trains will not run.