 On 9 February 2007, Stewart became assistant manager to his own former assistant Owen Coyle at St. Johnstone, replacing Montrose-bound Jim Weir.On 22 November 2007, Stewart became caretaker manager of St. Johnstone when Coyle left to become the new manager of English club Burnley.Three days later, in Stewart's first – and only – game in charge, St. Johnstone won the 2007 Scottish Challenge Cup Final, their first cup win since the Scottish Consolation Cup of 1911, with a 3–2 victory over Dunfermline Athletic.