In late 2009, Kennedy was offered a three-year deal by the Sydney Swans. Kennedy accepted the offer, as the Swans' offered him more opportunity to play senior football than Hawthorn, who had many players similar to Kennedy. He was traded to the Swans along with teammate Ben McGlynn for 2009 AFL Draft picks 39, 46 and 70. Kennedy capped a fantastic year by finishing 3rd in the Sydney Swans Best & Fairest, behind winner Kieren Jack and runner-up Shane Mumford. Kennedy was also awarded the Paul Roos Award for best player in the finals series.
Kennedy followed up his outstanding debut year in Sydney with another very consistent season in 2011. Despite a relatively slow start, Kennedy hit top form in the 2nd half of the year to finish equal 2nd with Rhyce Shaw in the Bob Skilton Medal (behind winner Adam Goodes). Kennedy further enhanced his growing reputation around the league with 2 more outstanding performances in the Swans' finals games against St.Kilda and Hawthorn.
Kennedy had his most consistent year earning himself his first All-Australian team selection. Kennedy won the Brett Kirk Medal in round one. Kennedy polled in equal eighth place in the Brownlow Medal, with 19 votes - the most of any Sydney player. He played in Sydney's Grand Final winning team, where he had 26 disposals and kicked two goals. He also won the Sydney Best & Fairest (Bob Skilton Medal) with (877) votes to win by a massive 172 votes from 2nd Ted Richards (705) and 3rd Ryan O'Keefe (701), managing to consistently poll votes in each round.