Soon after retirement from playing, McNeill became a football manager. For a short time, he managed Clyde. He left Clyde after a short time for Aberdeen. He finished as a runner-up in the league and Scottish Cup with Aberdeen. Celtic manager Jock Stein left the club in 1978. McNeill soon became Celtic's manager. As Celtic manager between 1978 and 1983, he won three league titles, a Scottish Cup and a Scottish League Cup. He would go on to manage English sides Manchester City (1983–86) and Aston Villa (1986–87).