Born in Alexandria, West Dunbartonshire, McIntyre began his senior career in England, after having unsuccessful trials with Hearts and Dundee United, and serving a three-year joinery apprenticeship, signing for Bristol City in 1991. While there, he had a loan spell with Exeter City in 1993. Later that year he returned to Scotland, signing for Airdrieonians where he impressed to earn a move to the top division. In March 1996 he joined Kilmarnock, going on to be part of their Scottish Cup-winning team in 1997. McIntyre scored the winning goal in the semi-final replay against Dundee United.