Charles Horton is to resign as chief executive of Govia Thameslink Railway following months of controversy over delays and cancellations to services.
In a letter to staff, he said the company had been going through some "very challenging" times in recent weeks.
Services on GTR's Southern and Northern franchises have suffered huge delays since a new timetable was introduced last month.
David Brown, group chief executive of GTR's parent company, Go-Ahead, said: "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.
"We are committed to working with the Department for Transport and Network Rail to address recent problems and to deliver a reliable, punctual service for passengers."
Mr Horton said: "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.
"I am immensely proud of my team and I would like to thank my 7,000 colleagues at GTR for all their hard work over the past four years."
In his letter to staff, Mr Horton said: "In my view, this was an industry-wide failure of the timetabling process. But with leadership comes responsibility and so I feel it is only right that I step down.
"Before my departure in a few weeks' time, I will continue to work with my colleagues to ensure a smooth handover as we work to put our railway back on track and give our passengers a reliable service once again.
"Finally, I would like to say that I am very proud of all of you GTR colleagues. Our mission is the most challenging on the entire railway and I believe that in time the changes we are making will come to be recognised as a turning point which began to turn around the Southern, Thameslink and Great Northern routes after years of under-investment."