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 from dropping down at the end of the season. Shiels responded by making a number of big name signings, including Tommy Wright, Paul Beesley and Liberian international Leon Browne, but none of them proved a success and the club finished in fifth place. The club improved significantly in the 2002–03 season, although ultimately they managed only second place in the First Division, as well as the Ulster Cup and the Country Antrim Shield. The league position was enough to ensure promotion, although the club had led the table until near the end when Dungannon Swifts took over at the top.