[5] MacFarlane transferred to First Division club Airdrieonians in July 2001 and though his 2001–02 season was ended prematurely by a cruciate ligament injury,[6] he was a part of the team which was victorious in the 2001 Scottish Challenge Cup Final.

[5][7] Though still recovering from a cruciate ligament injury suffered while an Airdrieonians player, MacFarlane signed a one-year contract with Scottish Premier League club Heart of Midlothian in July 2002, on a part-time wage.

[15] A move to Dundee United was blocked by the Hearts board in August 2005 and after suffering a knee injury,[16][17] he made just one appearance under Burley's successor,[14] Graham Rix, before departing the club in January 2006.

[12][13] MacFarlane wound down his career with spells at lower division clubs Greenock Morton, Airdrie United and Annan Athletic and retired in 2011.

[3] MacFarlane began his coaching career in 2012 and served as assistant to former Heart of Midlothian teammate Steven Pressley at Falkirk, Coventry City, Fleetwood Town and Pafos.