Career
He became joint caretaker manager at Coventry City in February 2015, having previously worked as caretaker manager at Scottish Football League First Division outfit Falkirk from 2011 until early 2013. He stayed with the club after Tony Mowbray"s appointment as manager but left on 31 July. MacFarlane began his senior career in 1999 with before moving to Kilmarnock in 2000.
Failing to play a first team match for Killie, MacFarlane spent most of his single season at Rugby Park on loan with a spell back at and then another at Clyde.
Following his release in 2001, MacFarlane joined Airdrieonians, where he played nearly thirty league matches before a knee injury ended his season prematurely. Despite being injured, MacFarlane joined Hearts in July 2002, with manager Craig Levein signing the player on a part-time deal due to his injury problems.
MacFarlane made his debut at the end of November. and was awarded a new, full-time deal two months later. On transfer deadline day in August 2005, MacFarlane was on the verge of joining fellow SPL side Dundee United when the Hearts board cancelled the transfer, despite the player having already travelled to Tannadice to agree personal terms and undertake a medical.
Instead, MacFarlane was allowed to leave in the following window in January, where he secured a short-term move to Aberdeen.
After starting only two matches for the Dons, MacFarlane was told in late April he could leave at the end of the season and he subsequently joined Gretna a month later. After injuries restricted him to just eight appearances in his first season at Raydale Park, MacFarlane was released halfway through his two-year contract, leaving him free to join in June 2007. McFarlane was a mainstay of the Queens run to the final of the 2008 Scottish Cup beating Aberdeen 4–3 in the semi final.
The final was against Rangers at Hampden Park, Glasgow.
As the underdogs QoS put up an excellent showing only losing by the odd goal in five. MacFarlane, a lifelong Rangers supporter described it as the biggest match of his career and typically gave a committed and hard working performance.
In June 2009, MacFarlane signed for Greenock Morton, under freedom of contract. He was released by Morton on 31 August 2010.
After his release he played in one trial match for Airdrie United but failed to earn a contract at New Broomfield.
On 19 November 2010, Neil MacFarlane joined Annan Athletic. In August 2011, he was appointed first team coach at Falkirk, where he remained until March 2013, when he moved with Steven Pressley to become assistant manager at Npower Football League One side Coventry City F.C. On February 23rd 2015, following the departure of Steven Pressley, MacFarlane took over as caretaker manager alongside Dave Hockaday at Coventry City F.C.
In October 2015, MacFarlane was appointed Assistant Manager to Steven Pressley at Fleetwood Town Football Club. He also coached junior members.