Though it has the appearance of a standard two platform station on a double track line, it is actually sited east of Thornton West Junction, where the double line from Cardenden splits into two parallel single lines that diverge after passing through the station to join the main line. One of these runs southwards to Thornton South Junction and is used by all trains to and from Edinburgh via the coast, whilst the other curves to the north and is used by trains heading for Markinch and thence to Perth or . As a consequence of this, both platforms are bi-directional (a similar layout exists at in Lancashire) but the southern one (platform 1) is much busier than the northern one (2) due to the service pattern in use on the Fife Circle.