David Simpson, the state-owned concern's route managing director for Scotland, has been absent since shortly after a meeting with a representative of his London bosses last month.
A Network Rail spokesman has now confirmed that the highly-regarded executive will not be returning to his duties.
He said: "David Simpson, route managing director for Scotland, has left Network Rail with immediate effect.
"David Dickson, area director for the West of Scotland, will continue as acting route managing director until a replacement is recruited.
Previously Network Rail had said Mr Simpson was "on a period of extended leave owing to personal circumstances".
Mr Simpson has run Network Rail north of the Border since 2005.
It has had considerable devolution in its business since October 2011, reflecting political devolution at Holyrood, which is responsible for transport.
The Blantyre-born executive, who lives in Ayr, is a veteran of the former British Rail and has spent more than 25 years in the industry.
He served in senior roles in England for Railtrack, the semi-privatised rail infrastructure firm that predated Network Rail, and in rail freight firms.
He managed the UK's most important single railway, the West Coast Main Line from Glasgow to London via Manchester and Birmingham before securing the top Scottish job in 2005.