The station is situated on the Dunfermline Branch of the Edinburgh and Northern Railway, just west of its divergence from the E&NR main line via a triangular junction. It is a completely new structure, having been built by British Rail with the support of Fife Regional Council to serve the two communities that it is named after. Glenrothes (as a post-war new town) had never previously had its own station (though station is nearby) whilst Thornton had lost its station ("Thornton Junction") on the main line in October 1969 in the aftermath of the Beeching Axe (services on the line westwards to and on the Leven branch had ended at the same time).