John Stuart was born at Upper Strathspey, Moray. He was the second son of Donald Stuart (b.c.1740) of Leanchoil, then a farm situated on the edge of the Abernethy Forest, and his wife, Janet Grant (b.1743), daughter of Robert Grant of Cromdale. John Stuart's grandfather (brother of the 1st Laird of Cuilt) was descended from the 1st Laird of Auchtow, son of the Duncan MacRobert Stewart, 3rd Laird of Glenogle, Perthshire. As a Jacobite, his grandfather is thought after the Battle of Culloden to have sought refuge under the protection of Clan Grant in Moray, as he was originally from Balquhidder, Perthshire. John's mother was descended from the Chief of Clan Grant of Castle Grant and was a close cousin of the Robert Grant who co-founded the North West Company. John's sister, Barbera, was the mother of Lord Strathcona, and it was Stuart who had attained for him his first role in the Hudson's Bay Company.