Phil Verster is leaving his post as managing director of ScotRail Alliance to take up the same role of the East West rail project.
The 53-year-old, who has been in the post since May 2015, has been under intense pressure in recent months, because of the rail service’s failure to meet targets on punctuality and reliability.
Network Rail and ScotRail franchise operators Abellio said Mr Verster’s successor has been agreed and will be announced in the coming days.
He will take up his new post in the spring.
Mark Carne, chief executive of Network Rail said: “Phil has done a great job setting up the ScotRail Alliance and overseeing the delivery of one of the largest programmes of rail modernisation in Scotland since Victorian times.
“I am delighted that a leader of Phil’s calibre will be heading up the new East West rail project, recently announced by the Secretary of State. We have agreed a replacement to succeed Phil and will be making an announcement shortly.”
Dominic Booth, managing director, Abellio UK said: “Phil has played a key role in helping us create the ScotRail Alliance, the first time an operating company has come together in such a deep alliance with Network Rail to deliver the very best for our customers.
“We are currently investing in a fleet of 70 new trains, which will transform the rail travel experience of our customers.”
Mr Verster said: “Over the last two years I have worked with my team to launch the ScotRail Alliance, delivering hundreds of commitments and laying the ground for the exciting new train fleets that will start to arrive later this year.
“The opportunity to build on these same principles with the creation of a new business such as East West Rail is great for me and my family, and I wish the ScotRail Alliance team all the best for the future.”
East West Rail Link is a planned railway route linking the Great Western Main Line, Oxford, Bicester, Milton Keynes, Bedford, Cambridge, Ipswich and Norwich in England using part of the former Varsity Line.