After retiring from playing, McClair took on a coaching role at Blackburn Rovers before returning to Manchester United, where he spent several years as Youth Academy Director.

[19] Despite competition from Alan McInally and Mark McGhee, McClair and Johnston remained the regular pairing playing up front for Celtic.

This culminated in a memorable final-day 5–0 win over St Mirren at Love Street, with McClair and Johnston both scoring twice as title-rivals Hearts capitulated to a 2–0 defeat at Dundee.

Despite a bright start to the campaign from Celtic, the team's form began to fade during the winter months and they squandered a nine-point lead in the league, which was won by Rangers.

Celtic initially wanted £2 million for him, a fee which would have made him the most expensive player at the time to have signed for any British club, whilst Manchester United had offered only £400,000.

[32] He put a further double over Sheffield Wednesday in the March return game at Old Trafford,[33] and scored a hat-trick against Derby County in early April.

He could have had even more, but his late penalty miss at Arsenal in the FA Cup fifth round[38] meant that Manchester United were eliminated with a 2-1 loss in what was a trophy-less season.

By the end of November, however, McClair had scored just twice in the league, whereas Hughes had found the net eight times, with Manchester United finding themselves in mid-table after a run of eight draws and one defeat.

Results improved over the next couple of months as United crept to the fringes of the title challenge, but fell away in the final quarter of the season as the club finished 11th.

He was now facing competition from highly promising young striker Mark Robins,[40] who had scored 10 goals in 23 first team games that season.

In October 1990, McClair was involved in controversy when in reaction to a late challenge he repeatedly kicked Arsenal's Nigel Winterburn in the back as he lay prone on the ground, sparking a 21-man brawl.

The two had a history, as Winterburn had been seen mocking McClair after his penalty miss in the FA Cup fifth round three seasons before, which earned the Arsenal player a lot of criticism.

[47][48] Alex Ferguson then made unsuccessful bids for strikers David Hirst[49] and Alan Shearer,[50] before signing Dion Dublin, who was bought as backup for McClair and Hughes.

In 1993–94, the first season where he was no longer considered a first team regular, he appeared in 26 league games (though started just 12 of them) and scored one goal.

He was still receiving playing time in 1996–97, and on the first day of that season, McClair was credited with an assist for David Beckham's spectacular goal from the halfway line against Wimbledon.

[57] He scored a total of 127 goals for Manchester United, the last two coming against Coventry City in a 4–0 away league win on 22 November 1995, although he made some 60 first team appearances over the next two and a half years (mostly as a substitute).

The match was a qualifier for Euro 88, and McClair played in midfield behind his Celtic teammate and striker partner, Mo Johnston.

Despite his omission, McClair continued to feature regularly for Scotland and represented his country at the 1992 European Championships, where he scored his first international goal in a 3–0 win over the CIS (formerly USSR).

After a year of shadowing Les Kershaw, McClair replaced him as the director of the Manchester United youth academy at the start of the 2006–07 season.

[74] McClair left Manchester United after being appointed by the Scottish Football Association in February 2015 as their national performance director, effective from 1 June 2015.