Stewart was the son of John Stewart, 3rd Earl of Atholl and Grizel Rattray. He supported the government of the queen dowager Mary of Guise. He wrote to her on 10 June 1554 describing a skirmish in which his cousin George Drummond of Ledcrieff was killed by the lairds of Ardblair, Drumlochie, and Gormok, his followers. Lord Ruthven, sheriff of Perth, and Lord Drummond had searched for these lairds in vain but arrested six innocent poor men, who also depended on him. He hoped she could arrange a fair trial for them in Edinburgh or Perth, especially because Lord Ruthven favoured the Drummonds. He was coming to see her, but had fallen ill and wrote from Tullibardine. Subsequently, Patrick Blair of Ardblair was found, tried, and beheaded for the murder. In 1560 he 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. On the arrival of Mary, Queen of Scots, from France in 1561 he was appointed one of the twelve privy councillors, and on account of his religion obtained a greater share the queen's favour than either Murray or Maitland. He was one of the principal supporters of the marriage with Lord Darnley, became the leader of the Roman Catholic nobles, and with Knox obtained the chief power in the government, successfully protecting Mary and Darnley from Murray's attempts to regain his ascendancy by force of arms. According to Knox he openly attended mass in the queen's chapel, and was especially trusted by Mary in her project of reinstating Roman Catholicism. The fortress of Tantallon was placed in his keeping, and in 1565 he was made lieutenant of the north of Scotland. He was described the same year by the French ambassador as “très grand catholique hardi et vaillant et remuant, comme l'on dict, mais de nul". After the murder of David Rizzio, in 1567, he joined the Protestant lords against Mary, appeared as one of the leaders against her at Carberry Hill, and afterwards approved of her lavish imprisonment at Loch Leven Castle. In July he was present at the coronation of James, and was included in the council of regency to Mary's abdication. He, however, was not present at Langside in May 1568, and in July became once more a supporter of Mary, voting for her divorce from Bothwell. In March 1570 he formed with other lords the joint letter to Elizabeth asking for the queen's intercession and supporting Mary's claims, and was present at the convention held at Linlithgow in April in opposition to the assembly of the king's party at Edinburgh. In 1574 he was proceeded against as a Roman Catholic and threatened with excommunication, subsequently holding a conference with the ministers and being allowed till midsummer to overcome his scruples. He had failed in 1572 to prevent Morton's appointment to the regency, but in 1578 he succeeded with the earl of Argyll in driving him from office. On 24 March, James took the government into his own hands and dissolved the regency, and Atholl and Argyll, to the exclusion of Morton, were made members of the council, while on the 29th Atholl was appointed lord chancellor. Subsequently, on 24 May, Morton succeeded in getting into Stirling Castle and in attaining his guardianship of James. Atholl and Argyll, who were now corresponding with Spain in hopes of assistance from that quarter, then advanced to Stirling with a large force, when a compromise was arranged, the three earls being all included in the government. While on his way from a banquet held on 20 April 1579 at Stirling Castle on the occasion of the reconciliation, Atholl was seized with sudden illness, and despite the attentions of the court physicians Gilbert Moncreiff and Alexander Preston, and a Highland practioner recorded as the "Irland Leeche", he died on 25 April at Kincardine. There was a strong suspicion of poisoning. Some suspected Regent Morton or Annabell Murray, Countess of Mar. He was buried at the High Kirk of Edinburgh near the tomb of Regent Moray at the request the King.
