After his playing career O'Neill began a career in football management, initially with non-league Wycombe Wanderers. He later managed Norwich City but resigned on a matter of principle and joined Leicester City in the second half of the 1995/1996 season. He achieved great success at the club, gaining promotion to the Premiership in the same season as joining the club via the play-offs. Leicester finished in the top half of the Premiership in every season O'Neill was manager. He won the League Cup with Leicester in 1997 and 2000.
Since 2000 he has been manager of Glasgow Celtic F.C, taking the team to the final of the 2003UEFA Cup.
Martin O'Neill was awarded an OBE "for services to sport" in 2004.