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John Stewart, 5th Earl of Atholl, (1563–1595), Scottish landowner.
John Stewart was the son of John Stewart, 4th Earl of Atholl and Margaret Fleming, daughter of Malcolm Fleming, 3rd Lord Fleming and Janet Stewart.
He rescued the widowed Agnes Sinclair Countess of Erroll in October 1587. She had been violently abducted from her house at Inchestuthill and assaulted by Colin Campbell of Glenlyon and his followers.
In January 1580 he married Marie or Mary Ruthven, daughter of William Ruthven, 1st Earl of Gowrie and Dorothea Stewart.
They became friends with Anne of Denmark and while they were at Falkland Palace invited her stay with them at Dunkeld in July 1592. James VI of Scotland after some hesitation would not allow her to make the trip. Anne was unhappy at this and wished she was back home in Denmark with her mother Sophie. There were suspicions that the Earl had been involved in the rebel Francis Stewart's assault on Falkland Palace in June.
The English diplomat Robert Bowes hoped that they would persuade Marie's sister Margaret Ruthven to marry the son of the Master of Forbes. This would weaken the power of the Earl of Huntly. However, Margaret married John Graham, 4th Earl of Montrose.
On 11 November 1594 the Earl and his wife with their armed followers went to Moircleuch, and besieged the castle of Walter Leslie. He surrendered and they brought him back to their castle at Blair Atholl and imprisoned him there, under the care of George Leslie captain of Blair.
Atholl died in September 1595 and was buried at Dunkeld on 11 October.
On his death in 1595 Atholl left four daughters, Dorothea, Mary, Jean, and Anne, but no male heir, so the Atholl earldom reverted to the crown by "non-entry" and was given by James VI to Anne of Denmark.
In March 1596 John Stewart 6th Lord Innermeath married the earl's widow Marie Ruthven and in May 1596 he was newly created Earl of Atholl, after the countess had bought back the rights to the earldom for £10,000 Scots.
Marie Ruthven and her new husband arrested Agnes McCawis and Bessie Ireland as suspected witches. The two women accused two more women from Dunkeld of witchcraft, Margaret Stewart and Isobel Douglas, who complained of their unjust imprisonment to the Privy Council of Scotland. Marie Ruthven and the Earl were ordered to bring the four women to Edinburgh.