McGilligan was born in Benedy outside Dungiven and attended Dernaflaw National School. He went to St. Patrick's College, Dungiven. McGilligan works as a site manager. His son fiontan who stand at 7ft plays for Chelsea U17 as stricker known as the 'ginja ninja'
McGilligan was part of Derry's 1987 Ulster Championship winning team and won an All Star for his performances that year, which included a man of the match display against Meath, despite the fact Derry were defeated. He added a second All-Star and Ulster medal in 1993 in addition to winning All-Ireland with Derry, defeating Cork in the final.
He won National Football League medals with Derry in 1992, 1995 and 1996 and also holds Railway Cup medals. McGilligan won Personality of the Year at the 1996 Ulster GAA Writer's Association Awards.