After retiring from playing Mulgrew continued his involvement in the game as a manager. He led St Eunan's to several senior county titles and was part of
Declan Bonner's backroom team during Bonner's first spell as Donegal manager in the 1990s. In 2004, Mulgrew was appointed manager of the
Fermanagh senior team, and in his first season in charge he led them to the All-Ireland semi-final for the first time in their history. In 2006, he led them to Round 4 of the All-Ireland Qualifiers but Fermanagh were no match for Mulgrew's native Donegal. He left the Fermanagh job in 2007, following a narrow All-Ireland qualifier defeat to
Meath, saying "I've been dreading the prospect of this [leaving the job] because I bonded so well with this group of lads. But I always made clear that this was going to be my final year". Mulgrew was interviewed for the role of Donegal senior manager in 2007 following
Brian McIver's resignation, though McIver was reappointed after reapplying when he decided to carry on. Mulgrew then became involved in a public feud with former Donegal teammate
John Joe Doherty, concerning the Donegal managerial job when it became available again in 2008. Speaking on local radio on 24 October 2008, Mulgrew said: "To be classified as a former team-mate by that guy -- as far as I'm concerned, I'm not a former team-mate (of his)." Mulgrew had on this occasion been seeking a joint managerial position with the senior footballers alongside
Declan Bonner but both ultimately lost out to Doherty. ==Honours==