St Mirren MacPherson was then appointed as player/manager on 18 December 2003 after the resignation of
John Coughlin. He retired from playing to concentrate solely on management at the end of the
2003–04 season. MacPherson guided St Mirren to second in
2004–05 finishing behind
Falkirk. This was a significant improvement for the club having finished seventh the previous season. In the
following season MacPherson guided St Mirren back to the
Scottish Premier League having finished top of the First Division. He also guided the team to a 2–1 win in the
Scottish League Challenge Cup final against
Hamilton Academical with
Simon Lappin and
John Sutton netting the goals, becoming the only St Mirren manager to win a domestic double. In the
2006–07 season he retained St Mirren's place in the SPL, following a brief relegation fight. In the second last game of the season St Mirren's place in the SPL was confirmed courtesy of a 3–2 win over
Motherwell despite having been 2–0 down. This coupled with other results saw one of MacPherson's former clubs, Dunfermline relegated to the First Division. In
the following season and being continually challenged with budgetary constraints, MacPherson became the first St Mirren manager to be knocked out of both the
Scottish League Cup and
Scottish Cup by teams from a lower league in the same season. Despite these set-backs he retained St Mirren's SPL status with 10th place in the division. This was St Mirren's highest finish since
the 1990–91 season, finishing one place above MacPherson's former club Kilmarnock and relegated
Gretna. In the
2008–09 season he led St Mirren to a win over
Rangers at
Love Street with
Stephen McGinn netting the only goal of the game. Also in the same season he led St Mirren on a run of four unbeaten games, resulting in him receiving the
SPL manager of the month award for December 2008. He also guided them to the semi-finals of the
Scottish Cup, beating
Celtic 1–0 in the quarter-finals. St Mirren were in a five club relegation battle, but a penultimate weekend win away to Falkirk, almost guaranteed safety. St Mirren stayed in the top flight on goal difference, two goals better off than Inverness. In January 2010, after
Jim Jefferies left Kilmarnock, MacPherson became the longest serving manager in the SPL. On 11 May 2010, St Mirren announced that they had parted company with MacPherson.
Queen of the South In June 2011, MacPherson was announced as the new manager of
Dumfries club,
Queen of the South on a one-year contract. His assistant manager was announced as
Andy Millen. MacPherson left the club after they were relegated to the Second Division in April 2012.
Queen's Park MacPherson was appointed manager of
Scottish League Two side
Queen's Park in January 2014. He led the Spiders to promotion to
Scottish League One through the play-offs in his second full season in charge beating
Clyde over two legs in the playoff final. He left St Mirren in August 2020.
Greenock Morton In March 2021, MacPherson was appointed manager of
Scottish Championship side
Greenock Morton until the end of the 2020–21 season. He led the Ton to safety after winning the
Scottish Championship play-offs beating
Airdrieonians in the two-legged final in May 2021. McPherson parted company with Greenock Morton on 4 December 2021, with the team sitting in 8th place (ahead of the relegation places on goal difference). ==Managerial Record==