Stewart was the son of John Stewart, 3rd Earl of Atholl and Grizel Rattray. He supported the government of the queen dowager, and in 1560 was one of the three nobles who voted in Parliament against the Reformation and the confession of faith, and declared their adherence to Roman Catholicism. Subsequently, however, he joined the league against Huntly, whom with Murray and Morton he defeated at Corrichie in October 1562, and he supported the projected marriage of Elizabeth with Arran.