Refers to a person who follows a different religion, often from the perspective of a dominant faith. Can carry a negative or exclusionary tone depending on context.
In medieval Europe, pagans were often persecuted.
From a Christian perspective, he is a heathen, but he himself values his own faith.
Compound of 異 (i, 'different') + 教徒 (kyōto, 'believer of a religion'). The term is straightforward and transparent in meaning.