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 "verychallenging" times in recent weeks.
I recognise that passengers have been hugely frustrated at the significant disruption caused by the introduction of new timetables. It is the right time to hand leadership of GTR to a new pair of hands.
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.
I would like to thank Charles for his hard work with Govia for the past 15 years. Under often challenging conditions, he has built a team to deliver the largest railway change programme for decades, on a franchise that is not only the UK's biggest, but which has also has seen the highest passenger growth.
Meanwhile the RMT union has called for GTR to be stripped of its franchise.
For well over two years now RMT members fighting to defend safety and access have been subjected to abuse and hostility under the regime led by Charles Horton.