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As a player Clark started his career at Newcastle United. In 1993 he was part of the Newcastle side promoted to the Premier League and helped them finish second two seasons in a row.
He moved to Sunderland in 1997, and was part of the side promoted to the Premier League in 1999 with a (then) professional league record of 105 points.
Clark then joined Fulham in 1999 where he collected another Division One title medal in 2001.
In 2004, he helped Fulham secure what was, at the time, their highest final position - ninth in the top flight.After leaving Fulham in 2005, Clark returned to Newcastle, coaching and playing on a month-by-month contract.
On 1 June 2006, Newcastle manager Glenn Roeder appointed Clark as a first team coach and as reserve team manager.
In November 2007 he left his post at Newcastle to rejoin Roeder at Championship side Norwich City as assistant manager.
In December 2008, Clark was unveiled as the new manager of Huddersfield Town signing a three-and-a-half year contract replacing Gerry Murphy who was caretaker manager.
He would go on to lead the club to a ninth place finish in League One, in the 2008/09 season. Then in his first full season, Clark led Huddersfield to the play-offs where his side narrowly missed out in the semis to eventual winners Millwall. Remarkably Clark won the manager of the month award three times in 2009/10.Clark would once again improve his side's league position the following campaign, as Huddersfield finished 3rd in npower League One. He led his men on a remarkable club record 27 game unbeaten run, at the end of the season, just missing out on automatic promotion. After finishing third, Huddersfield then reached the play-off final only to miss out on a place in the Championship to Peterborough.
In 2011/12 Clark created history with Huddersfield by setting a new record for unbeaten matches in the npower Football League, surpassing the 42 unbeaten matches set by great Brian Clough in 1977-1978.
Despite his successes with the club, Huddersfield parted company with Lee in February 2012 whilst they were in strong contention for promotion by being just four points off the automatic places.
Later, in his first campaign in charge at St Andrews, he guided Birmingham to a 12th place finish in the Championship. In 2013/14, he secured their Championship status on the final day of the season. He remained with the club until October 2014 before joining Blackpool that same month.
Most recently, Clark has managed Kilmarnock and Bury.