The “significant bottleneck” of Carstairs junction in South Lanarkshire – where trains from Edinburgh have to slow to 15mph to join the west coast main line – would be included in the plans for improvements.
Virgin has also pledged more standard class seats by removing a first class carriage and better wi-fi as part of the new west coast contract from Sunday until March 2017.
A £35 million spending package by Virgin will also include improvements to catering on trains, and to waiting rooms and seating at intermediate stations on the routes, including free wi-fi.
The UK Department for Transport (DfT), responsible for the franchise, said Virgin had committed to working with bodies such as Network Rail “to look at how further improvements in journey times can be made from London to Scotland.
“This includes work to remodel Carstairs junction, a significant bottleneck.”
Improving the junction would also benefit CrossCountry and ScotRail services.
Virgin’s current fastest train between London and Glasgow takes four hours and eight minutes, but many take four-and-a-half hours or more.
Public transport group Transform Scotland welcomed the news, board member Paul Tetlaw saying: “We’re delighted to hear that as part of the franchise extension the bottleneck at Carstairs is to be tackled.
“It is scandalous it has taken so long to address this issue.”
A Scottish Government spokesman said: “As we announced in April, in recognition of the strategic importance of Carstairs junction and the benefits it could bring to the railway, the Scottish Government has agreed to fund Network Rail’s development of detailed engineering plans for remodelling of the junction and the associated business case.”
A spokesman for Virgin Trains said: “Network Rail is looking at line speed improvements, including remodelling of Carstairs junction, which, taken together, would facilitate a sub-four-hour, non-stop journey between Glasgow and London.”
The franchise, which carries 32 million passengers a year, includes trains between Glasgow, Edinburgh and London on the west coast line.
Virgin said it was cutting first class seats as first-class passenger growth was slower than that of standard class.
The short-term deal comes after the DfT abandoned a planned west coast main line passenger franchise in 2012, which it had awarded to FirstGroup, after admitting civil servants had botched the bidding.
Virgin, which has held the contract since 1997, was initially given an interim extension until this year. A new long-term franchise is due to start in 2017.
Virgin will pay £430m to the UK government for the new contact – 58 per cent more per year than currently.
UK Transport Secretary Patrick McLoughlin said: “This deal will provide thousands more seats and better journeys for the tens of thousands of passengers who use these services every day.”
However, Mick Cash, of the Rail, Maritime and Transport union, said: “The collapse of the tendering process on the west coast has allowed Virgin to bully themselves into a monopoly provider position.”