Lee Clark was appointed as Norwich City's Assistant Manager on 2nd November 2007 after Glenn Roeder persuaded him to leave Newcastle, where he was reserve team manager. and join City.

Clark began his career at Newcastle in 1990 and became a huge hero to the St James' faithful during his first seven-year spell there. He made 193 appearances for United scoring twenty three goals. He then made the rare move to local neighbours and bitter rivals Sunderland although, after 74 appearances, his career on Wearside came to an end after he wore a derogatory T-shirt at the 1999 FA Cup final.

He moved south to Fulham, playing almost 150 games before being allowed to leave at the end of 2005, turning up at St James Park again as a player under Graeme Souness' management.

When Roeder replaced Souness at the helm of Newcastle United. Clark was drafted into the coaching side eventually becoming reserve team manager

Sam Allardyce sent Lee his blessing saying “Lee's a good lad, he's been fantastic. He wants to move on and gain the experience to help him ultimately achieve his aim of becoming a manager one day. It's a big step for him but I hope it goes well for him.”

In Novemebr 2008, Lee was linked with the vacant manager's position at Carlisle United, following the departure of John Ward. At the end of November, it was reported by The People that Lee had been interviewed for the managerial position at Huddersfield. This rumour proved true with Clark taking up the Huddersfield manager's position on 10th December 2008 once the Canaries and the Terriers had agreed compensation.

Glenn Roeder said he was not surprised at Clark's rapid progress from player, to coach and now potentially to his first managerial role: "I always knew from day one when I first appointed Lee as Reserve Team Coach at Newcastle how ambitious he was to become a manager one day, probably sooner rather than later. At that stage he was just completing his A licence and today he's just about to complete his pro licence, which hes been doing with the Northern Ireland FA. So today's news about Lee joining Huddersfield as their new manager has really come as no surprise to me. I feel he has enough experience to be his own man now and he goes with my best wishes and a big thanks for the part he played last year in helping the Club to secure its Championship status."

After two consecutive seasons where Huddersfield reached the League One play-offs, Clark was highly rated as a manager and was linked in October 2011 with the vacancy at Leicester City whose big-spending manager Sven Goran-Eriksson was sacked after his team lost heavily to Millwall.

On 19th November 2011, Clark's Huddersfield set a new Football League record by going 43 games unbeaten when they defeated Notts County 2-1 despite having striker Alan Lee sent off. The Terriers had matched Nottingham Forest's Football League record of 42 games unbeaten when they drew with Walsall two weeks previously. This latest result leaves them just six short of matching Arsenal's English record of 49 league games unbeaten, which included going the whole of the 2003-04 Premier League season without defeat

On 15th February 2012, Huddersfield sacked Clark and his coaching staff despite the Terriers sitting in fourth place in League One. "I am very perplexed as to why I was dismissed as manager of Huddersfield," said Clark in a statement issued by the League Managers' Association. "I'm extremely disappointed and shocked considering we're in a great position to compete for automatic promotion." Supposedly relations between the board and the manager had turned sour in previous months despite the Terriers' good form

Lee was quickly linked to the vacant Norwich position following Paul Lambert's departure to join Aston Villa at the beginning of June 2012. Instead he was appointed as Birmingham manager on 26th June 2012, replacing Chris Hughton who had joined Norwich. Clark has appointed Terry McDermott as his assistant manager and is also hoping to bring in Derek Fazackerley as first-team coach. McDermott and Fazackerley left in February 2014 when Clark appointed his former Newcastle teammate Steve Watson as assistant.

On 20th October 2014 Clark and Watson were sacked by Birmingham with the club lying in 21st place in the Championship. Thye had won only one home game since October 2013.

Clark wasn't out of work for long as he was appointed Blackpool manager on 30th Octobe 2014 on a one year rolling deal. "The main objective is to try and keep the club in the Championship and build from there. It is a big challenge because of our position in the league, but it's a challenge that can be overcome.I'm very confident with the players I've got here, in what we can do going forward, that we can achieve those goals." said Clark. "We needed someone with experience of the Championship and that's what Lee brings to the club," said chairman Karl Oyston. "Lee's done remarkably well in a difficult background at Birmingham.
"We needed someone to come in and organise us properly and bring in the structure, approach and positivity that we've been lacking."

Unfortunately Clark could not save Blackpool and they were the first team in the Football League to be relegated when they went down on 6th April 2015 folloiwng a win by fellow strugglers Rotherham against Brighton. Clark left the club at the end of the season.

In October 2015, Clark was linked with the managerial vacancy at Doncaster Rovers.

On 15th February 2016, Clark was appointed manager of Scottish side Kilmarnock replacing Gary Locke.

Clark quit Kilmarnock on 15th February 2017 to take charge at League One side Bury replacing Chris Brass. "Lee is someone who I have followed through his playing and managerial career," said Shakers chairman Stewart Day. "I firmly believe that Lee is the right man and he has an enthusiasm and passionate desire to take this club forward. I was overwhelmed with his knowledge of the club and the contacts he has in the game and how he believes in what we can achieve together." Clark had won 10 of his 44 games at Kilmarnock. Assistant Lee McCulloch will become interim manager of Kilmarnock, with Peter Leven as his No.2. Clark won his first game with Bury - a 2-1 away win at Chesterfield.

Clark was sacked as Bury manager on 30th October 2017. The Shakers' defeat to Doncaster on 28th October was Bury's fourth successive defeat, leaving them 23rd in the League One table with 12 points from 16 games.Clark won only nine of his 33 games as Shakers boss

On 1st June 2019, Clark was appointed manager of National League North side Blyth Spartans. Clark said "I've been too long out the game and it's an opportunity to be at home around my family at a great club with great tradition. When they contacted me I was honoured."

He left Blyth by mutual consent,along with his assistant Paul Stephenson on 4th March 2020 and was replaced by Michael Nelson. The Spartans were second bottom of the table at the time with Clark's requirement to build the squad from scratch being unsuccessful.

After a spell with Newcastle Blue Star, he was appointed manager of Sudanese club Al-Merrikh on March 6th 2021. His appointment came just hours after they sacked Nasreddine Nabi for drawing 0-0 with Simba FC (Tanzania) in the African Champions League, leaving them bottom of their group. Al-Merrikh are based in Omdurman, the largest city in Sudan. Founded in 1908, they are one of the biggest clubs in Sudan and have been national champions 21 times. Clark isn’t their first manager to have Norwich connections. Glorious Canaries reports that John Manning, who made 67 appearances for City in the late 1960s, spent a year as Al-Merrikh’s manager.

He took charge of his first game - a 2–1 win over Hilal Al-Fasher in the Sudan Premier League on 9th March 2021. Clark's first experience of the CAF Champions League was a 3–0 away defeat to Simba of Tanzania on 16th March 2021 after which he blamed the loss on 'sabotage'. On 19th June 2021, Al-Merrikh announced Clark had resigned as manager.

In November 2021 he was appointed as manager of Al-Ittihad in the Oman Professional League.