However, proposed open access services between Peterborough and Doncaster by WAGN were rejected by the Office of Rail Regulation (ORR) due to a lack of capacity.

[4][5] On 5 January 1997, West Anglia Great Northern commenced operations, taking over service from British Rail, including their rolling stock.

[6] During the late 1990s, West Anglia Great Northern submitted an application to operate extended services on an open access basis between Peterborough and Doncaster; however, the proposal was rejected by the Office of Rail Regulation (ORR) due to a reported lack of capacity on the route.

[8] During July 2000, it was announced that Prism Rail, and thus West Anglia Great Northern as well, had been acquired by the British transport conglomerate National Express in exchange for £166 million.

[13] On 10 May 2002, a major rail accident involving a northbound WAGN service occurred at Potters Bar, resulting the deaths of seven people and the injury of a further 76.

[18] West Anglia Great Northern operated all-stops and limited stops West Anglia services out of London Liverpool Street to Chingford, Enfield Town, Hertford East, Stansted Airport, and Cambridge, and all-stops and limited stops Great Northern services out of London King's Cross to Cambridge, King's Lynn and Peterborough, including the Hertford North loop line.

Dedicated bicycle and wheelchair spaces and improved lighting were also provided, while the exterior received a new white, grey, blue and red livery.

[27][28] In December 2005, the Department for Transport awarded the Thameslink franchise to FirstGroup with the services operated by West Anglia Great Northern transferring to First Capital Connect on 1 April 2006.