Following his retirement from playing, Kennedy began coaching with the Ipswich Town academy in 2012. He was appointed as the club's under-21's head coach in 2012. He managed the Ipswich under-21 side from 2012 to 2016 before leaving to take up a position coaching in Manchester City's academy. Kennedy was a coach with Manchester City from 2016 to 2018, before being released as part of a restructuring process within Manchester City's academy. He also spent time coaching with Wolves' under-23 side in 2019.