The article for the train on Pottermore seems to indicate that the track has been hidden by a concealment charm. However, it isn't entirely clear if this is the whole track, parts of it or the charm was used in the operation to get the train.
A daring and controversial solution to the thorny problem was finally suggested by Minister for Magic Ottaline Gambol, who was much intrigued by Muggle inventions and saw the potential in trains. Where exactly the Hogwarts Express came from has never been conclusively proven, although it is a fact that there are secret records at the Ministry of Magic detailing a mass operation involving one hundred and sixty-seven Memory Charms and the largest ever mass Concealment Charm performed in Britain. The morning after these alleged crimes, a gleaming scarlet steam engine and carriages astounded the villagers of Hogsmeade (who had also not realised they had a railway station), while several bemused Muggle railway workers down in Crewe spent the rest of the year grappling with the uncomfortable feeling that they had mislaid something important.
Pottermore, The Hogwarts Express
Using some reasoning though I think it to be possible that the start of the track is concealed which then joins onto a normal muggle track through a concealed junction. A similar situation would then occur at the end point. Of course this is just speculation and the above quote could mean that the whole track is in fact under the concealment charm.