Matty Kennedy first game for "Killie" in a 2–1 win over St Mirren at Rugby Park on 2 January 2012. He ended the 2011–12 campaign with 11 Scottish Premier League appearances. He played three games at the start of the 2012–13 season before leaving the club; manager Kenny Shiels expressed his concern that Kennedy had left Kilmarnock too soon and he had missed out on seeing Kennedy's "proper development" at the club. On 31 August 2012, the final day of the summer transfer window, Kennedy signed for English Premier League side Everton for a "nominal fee". The fee was later revealed to
Kenny Shiels the club, having a rejected a move from an English club in the past week. A week later, on 22 May 2012, Shiels signed a two-year contract extension. At the start of the 2012–13 season, Shiels was given two-match touchline ban by the SFA in June, having served one suspension on the last game of the season and miss one match at the opening game of the season. His touchline ban was given over commenting made about a referee's decisions made in a match between Celtic and St Johnstone. Following a controversial penalty in a 2-0 defeat against Hibernian on