In March 1998, McIntyre was transferred to Reading for a fee of £440,000, and the following month appeared for Scotland in a 'B' international against Norway. He appeared as a late sub to replace Andy Smith. He played in the 2000/01 third tier play off final defeat in extra time. This was his last game playing in English football. He returned to Scottish football, signing for Dundee United in July. Although his initial contract was for a two-year period, he twice extended his stay at Tannadice and again was a goal scorer in a Scottish Cup semi final winning team. It was announced by United manager Craig Brewster in April 2006 that McIntyre would be free to leave the club at the end of the season.
In July 2006, McIntyre signed for Dunfermline after negotiating a termination of his United contract. He scored a decisive penalty kick against Hibernian at Hampden Park in a Tennents Scottish Cup Semi-final replay allowing Dunfermline to progress to the Final with a 1–0 Victory. After being appointed as Pars manager at the start of 2008, McIntyre did not make an appearance for the club until November 2008 due to injury.
McIntyre was appointed caretaker head-coach of Dunfermline Athletic on 4 December 2007, following the sacking of the incumbent manager of the club, Stephen Kenny. McIntyre's first match in charge was a home clash against Clyde on 8 December, when Dunfermline came from behind to claim a 1–1 draw, a result repeated the next week away at Partick Thistle, where Stephen Glass also missed a penalty. He was appointed as Dunfermline manager on a full-time basis on 3 January 2008, signing a two-and-a-half-year deal after an impressive run of four successive victories. After four straight wins, McInytre was awarded the First DivisionManager of the Month award for December. He again won the award, this time for Dunfermline's unbeaten run in September 2008. In the 2010–11 season, McIntyre led Dunfermline to the First Division Championship and promotion back to the Scottish Premier League, eventually winning the league by ten points, ahead of Raith Rovers. In three and a half years in the division with The Pars he was Manager of the Month five times. Dunfermline struggled in the 2011–12 Scottish Premier League season and were four points adrift at the bottom of the league table when he left the club in March 2012.
In April 2012, McIntyre was hired by Bristol City manager Derek McInnes to work as the club's first team coach until the end of the 2011–12 season. He had previously been doing some scouting work for Bristol City after being sacked by Dunfermline. McIntyre left Bristol City on 25 January 2013 by mutual consent. 
McIntyre was appointed Queen of the South manager on 27 June 2013, replacing Allan Johnston who moved to Kilmarnock on 24 June 2013.  McIntyre appointed Gerry McCabe his assistant manager on 28 June 2013, having previously assisted him at Dunfermline.