Stuart was born in Scotland in 1745 and began life there as John Smyth or John Ferdinand Smyth. He later wrote that he was the son of R. Wentworth Smyth, a gentleman who had fought in the Jacobite rising of 1715 and also the later one of 1745. According to Stuart’s account, in 1744 his elderly father married Maria Julia Dalziel, a widow of fifteen, as his second wife. He reported that his mother was a grand-daughter of General James Crofts, a natural son of the Duke of Monmouth, who was a son of Charles II, and that Wentworth Smyth was Monmouth’s son by Henrietta Maria Wentworth, a daughter of Thomas, Lord Wentworth, and grand-daughter of Thomas Wentworth, 1st Earl of Cleveland. Henrietta Maria had died in 1686, not long after Monmouth's execution, and Stuart said a Colonel Smyth, an aide-de-camp of Monmouth’s, had adopted her son and made him his own heir. Consequently, Stuart’s father had grown up in France, from where he returned to Scotland at the time of the 1715 Rising. Stuart stated in 1808 that he had been named for his godfather, Prince Ferdinand of Brunswick.