Kenny Shiels in May 2007, as their head of youth. He left Tranmere in June 2010 to become assistant manager at Kilmarnock, following his three-year stint at the club. After Mixu Paatelainen left Kilmarnock to become manager of the Finland national football team, Shiels became caretaker manager. His first game in charge was a goalless draw with St Johnstone on 2 April 2011. On 15 June 2011, he became manager of Kilmarnock on a permanent basis and upon being manager, he soon added Jimmy Nicholl as his assistant manager, who just quit Cowdenbeath. He helped Kilmarnock achieve their first home win against
Kenny Shiels at the end of the season. Alongside his club jobs, Shiels was also employed by the Irish Football Association to manage the Northern Ireland national under-17 football team, a role he retained, until 2007, when new senior manager Nigel Worthington brought in his own men at youth levels. Shiels took charge of Larne for the 2005–06 season and took the club to two cup semi-finals, but his full-time job with the IFA meant that he was unable to fully devote his time to the club and so he stood down at the end of the season. Shiels joined Tranmere Rovers