Charles Horton, chief executive of Govia Thameslink Railway, is to resign, the company has announced.
The company said Mr Horton will remain in post for a short period to oversee the development of a temporary timetable to address the recent major disruption to rail services.
In a letter to staff, he said the company had been going through some "very challenging" times in recent weeks.
Rail passengers have faced major disruption since the biggest timetable changes in history were introduced in Surrey, Sussex, Hampshire and Kent last month.
Every time of every train has changed as part of the £7 billion Thameslink upgrade.
The changes are designed to make trains more frequent and create more space for passengers.
Govia Thameslink will now run 3,600 services a day for over 900,000 passengers.
That's 400 more trains, creating room for an extra 50,000 people.
Meanwhile the RMT union has called for GTR to be stripped of its franchise.