3 months is not long; it might well clear up on its own.
He's 11 so it could be associated with the hormonal changes of a growing boy.
Or perhaps his skin doesn't like coming into contact with something such as man-made fibres, so change his pillowcase for a pure cotton one.
Also don't let him use soap to wash his face, it could be that. Nobody needs soap anyway unless they're a coal miner, so just use fresh water..