SCOTRAIL Alliance managing director Phil Verster is quitting to run a new type of railway in England.
He will lead the construction of a line between Oxford and Cambridge, whose trains and track will be even more integrated than in Scotland.
His surprise departure was seized on by opposition parties as being linked to ScotRail’s poor performance.
However, Mr Verster said he had been approached last year to become managing director of East West Rail.
ScotRail also stressed punctuality had improved over the last three months.
Mr Verster, 53, will be succeeded by Alex Hynes, managing director of Northern, which runs trains in the north of England, industry sources have told The Scotsman.
Northern was jointly run by ScotRail parent firm Abellio and Serco from 2013 to 2016.
Abellio said: “Phil will take up his new post in the spring. His successor has been agreed and will be announced in the coming days.”
Transport minister Humza Yousaf tweeted: “Wish Phil Verster well in next challenge he takes on. Last few periods we’ve seen improvements on our railways – determined to keep that going.”
Mr Verster said: “Over the last two years, I have worked with my team to launch the 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.”
A Scottish Government spokesman said: “We are grateful to Phil Verster for his hard work … our focus is not on individuals but helping the industry to deliver the best possible service for Scotland.”
Mr Verster joined as the first head of the ScotRail Alliance, which includes track owner Network Rail, in May 2015.
Scottish Labour leader Kezia Dugdale said: “It’s clear the relationship between the SNP and ScotRail has broken down. One man has walked, and the only man left standing is [transport minister] Humza Yousaf. He must address this ScotRail crisis.”