Kelly was made deputy mayor of Toronto, succeeding Doug Holyday in 2013 after Holyday resigned from Council to contest a by-election for the Legislative Assembly of Ontario.
Following the controversy surrounding Toronto Mayor Rob Ford's admitted substance abuse and further allegations of inappropriate conduct, the Toronto City Council voted on November 15, 2013, and November 18, 2013, to remove the non-statutory mayoral powers from Ford and grant them to Kelly for the remainder of Ford's term. This was unprecedented as usually the Deputy Mayor's role is largely ceremonial.