The life-long railwayman, who was one of the industry’s most highly-regarded figures, was put on “extended leave” early last month along with Anne-Marie Harmon, one of its executive group of senior managers.
Network Rail, which has a budget of almost £1 billion a year in Scotland, said she would be returning to work.
Mrs Harmon was promoted in 2012 from being [Scotland] route performance manager to change programme manager, which involves commercial activities such as preparations for the Commonwealth Games in Glasgow.
David Dickson, the firm’s area director for the west of Scotland, has been standing in for Mr Simpson as acting [Scotland] route managing director for the last month.
In a statement yesterday, Network Rail said: “David Simpson, route managing director for Scotland, has left Network Rail with immediate effect.
“David Dickson will continue as acting route managing director until a replacement is recruited.”
The company today refused to say why Mr Simpson had left.
A spokesman said: “We are not saying anything else. Anne-Marie is returning to work.”
The Scotsman revealed last month that Mr Simpson was believed to have failed to follow proper procedures in appointing Anne-Marie Harmon to her current role.
Network Rail’s action against the pair is understand to have involved its London-based network operations managing director Robin Gisby – Mr Simpson’s boss – travelling to Glasgow in early December.
The company said at the time that the pair were on “extended leave because of personal circumstances”.
On the promotion of staff, it said: “We have procedures in place that have to be followed.”
Mr Simpson has been highly regarded since he took over running of Scotland’s rail network in 2005 in one of Network Rail’s first and most significant devolution of power from London.
One senior rail executive told The Scotsman last month: “I felt very, very saddened. It’s come as a real shock. He is very well thought-of politically.”
Mr Simpson, from Blantyre in South Lanarkshire, has worked on the railways since joining British Rail as a graduate trainee after leaving Aston University in Birmingham.
He has since worked for Network Rail’s predecessor, Railtrack, including on the upgrade of the Glasgow-London west coast main line and the introduction of Virgin Trains’ tilting Pendolino trains on the route.
Mrs Harmon, who lives in Lanarkshire, had been a performance manager at Network Rail since 2005 before being promoted in June 2012.