Carstairs Junction in South Lanarkshire, where London services branch off towards Glasgow and Edinburgh, will be remodelled and resignalling work will take place by 2017.
The move will boost journey times and reliability.
Network Rail unveiled the project as part of a £37.5bn plan to run and upgrade the railway system between 2014 and 2019. It aims to provide 355,000 new train services to cope with up to 225 million new passengers by the end of the decade.
However, it was criticised as not nearly ambitious enough by Virgin Trains. The firm ditched its own plans to cut fastest journey times between Glasgow and London to under four hours by 2014 after its bid to retain the franchise last year was rejected.
Network Rail also risked the ire of Scottish ministers after refusing a request to keep at least one of the main rail arteries connecting Scotland to England open when work takes place, saying it may have to close both the West and East Coast main lines on Bank Holidays.
Other projects include the electrification of the Glasgow-Edinburgh line, constructing a 30-mile route between Edinburgh and Tweedbank in the Borders and improvements to the route between Aberdeen and Inverness, including two new stations at Kintore and Dalcross.
Track improvements to the Highland Main Line will lead to services connecting Aberdeen and Inverness to the central belt being cut by around 10 minutes.
The Carstairs upgrade, expected to take place between 2016 and 2017, will allow a 15mph speed limit for trains turning right to Edinburgh to be eased and top speeds of between 40mph and 50mph allowed.
The same improvement is due for trains between Glasgow Central and Edinburgh, also restricted to 15mph, while London-Glasgow services will go from a 95mph maximum to 110mph.
Virgin Trains, which won a 23-month temporary contract to operate London to Scotland services after the collapse of the West Coast franchise contest, had planned to spend £125 million on track improvements that would have allowed its tilting trains to reach 135mph, ahead of the current 125mph limit.
David Simpson, Network Rail's route manager for Scotland, admitted the proposals fell short of this but said it had not ruled out raising the maximum speed limit by 2014 on some of the straighter sections of the West Coast Line around Lockerbie.
Further work was needed to ensure drivers could react in time to signals while travelling at the higher speed, he said.
He added: "We are committed to cutting journey times for cross-border services to allow them to compete better with airlines and have worked closely with all four operators, particularly Virgin, to try to turn these aspirations into something tangible on the ground."
Chris Gibb, Virgin's chief operating officer, said: "The Carstairs remodelling will give us a few seconds [journey time saving] but it is not nearly ambitious enough.
"The plans are silent on any journey time improvements south of the Border. They include more detail on improvements to Croxley Green to Watford Junction services than services between London to Glasgow."
A spokeswoman for Transport Scotland, the Government agency which funds Network Rail north of the Border, said it looked forward to the Office of Rail Regulation scrutinising its spending plans.
On closing both lines, she said: "The High-Level Output Specification published by the Scottish Government was clear that, where a cross-border route needs to close for maintenance or works, the alternative route must remain open."
l There were no arrests over Christmas linked to the late night and early morning alcohol ban, although men were warned by police at 8.45am on December 29 over drinking on the Alloa to Glasgow Queen Street service.