He is being stalked in the modern sense of the word - that is, by a person who is obsessed with the PC and in his (her?) delusional mind believes the PC loves him or otherwise belongs to him. Alternately, the stalker could be a serial killer.
The PC is a runaway slave being pursued by his masters.
Another idea: Maybe it only seems like the PC is being hunted; the hunter actually is not a bad person, but perhaps an old friend or family member who is desperately trying to contact the PC, but is always one step behind him or cannot contact him openly for some reason. Alternately, the pursuer is an innocent that hero-worships the PC and the PC has been trying to give him the slip so that the innocent won't be in danger or otherwise get in the way.
The hunter is a monster that is attracted to something about the PC (for example, perhaps a monster attracted to necromantic magic and the PC cast a necromantic spell near it) and will tirelessly pursue him until either it or he is dead.
The PC tricked a demon or sold to it his soul and now it wants payback/payment.
OK, one more - the PC unknowingly has a magical disease or curse that makes him paranoid. To make matters worse, someone really is pursuing him - a wizard, cleric or paladin who is trying to help him.