Kenny Shiels the League Cup Final, where they upset the odds by beating Celtic 1–0, with Dieter van Tornhout scoring the crucial goal in the 83rd minute. Killie's joy was tempered by the death of Liam Kelly's father, Jack, who suffered a fatal heart attack at the final whistle of the game. On the win, Shiels stated the team "are thinking more about Liam (Kelly) than our triumphalism". He then told BBC Scotland's Jonathan Sutherland, winning the cup is "unbelievable", in addition "a great emotion" for the Kilmarnock's supporters. Following his side's historic cup win, Shiels announced his intention to stay at
Kenny Shiels lost consecutive matches to Limavady United in the Gold Cup and Linfield in the league, causing Shiels to tender his resignation. According to the official club website Shiels was manager of Moyola Park from January 1999 to December 2000, although these dates overlap in part with his time at Coleraine. Nonetheless Shiels was in charge of the club and even signed a youthful Ivan Sproule for them. Shiels next appointment was at Ballymena United, where he was confirmed in the managerial chair on 2 January 2001. The club were battling relegation and ultimately Shiels was unable to prevent the club