The deal is expected to bring £35m of passenger benefits including an extra 5,500 standard-class seats every day. Virgin will spend over £20m on modernising stations and upgrading waiting rooms.
All of the Virgin Trains Pendolino and Super Voyager trains will be kitted with superfast WiFi, marking the first major intercity deployment of 4G technology on the UK's rail network.
Virgin Rail Group promised to add extra ticket machines and upgrade its website. Customers who book using Virgin Trains website or the mobile app will now be able to gain nectar points by the end of the summer.
Martin Griffiths, Stagecoach Group chief executive and Virgin Rail Group Co-Chairman, said: "Our country has the leading railway in Europe and Virgin Trains has been central to driving forward innovations that are now commonplace across the network.
"This new commercial contract shows that a well-run franchising system, with the public and private sectors working together, can deliver significant benefits to all stakeholders".