Watson started his career as a trainee with his local side Tottenham Hotspur. Watson scored his only Spurs goal on his debut in a League Cup tie against Brentford. As a youngster his first-team opportunities were limited and he went out on loan to several sides to build his experience, namely Brentford, Bristol City and Barnet. In 1996, he was signed by Swindon Town manager Steve McMahon. Newly promoted to second tier of the English Football League – Watson helped them avoid relegation. Watson moved on to Rotherham United in July 1999, astute Millers' manager Ronnie Moore signing him on a free transfer. In his first season Watson helped Rotherham to promotion from League Two, narrowly missing out on the title. Another promotion followed in the next season and Rotherham were promoted again into the Football League Championship. A key part of their rapid acceleration, Watson helped guide the team to survival by the narrowest of goal-difference margins. After over 100 games at Rotherham his knack for promotions was spotted by then Reading manager Alan Pardew who at first, took Watson on loan before signing him permanently in March 2002 for £150,000 – where he promptly repeated the trick, guiding the Royals to promotion from League One, in his now customary second place. His first full season at Reading saw the Royals into a play-off place, where narrow defeat to Wolves cost them a place in the Premiership. Perhaps tellingly Watson was on the bench for those key play-off games. When former teammate Phil Parkinson was installed as manager at Colchester United one of his first acts was to bring Watson to Layer Road. Marshalling the midfield Watson played a key role as in his first full season the U's stormed to promotion from League One, finishing in second place. Now with over 100 games for the U's under his belt he has been a key part of "The Best Col U ever" as the underdog U's finished their first season in the Football League Championship in 10th place. He was released by Colchester at the end of the 2007–08 season, and then signed on a free transfer for Luton Town. However, Watson failed to make an impact at Luton as a result of a knee injury that kept him out of action for much of his contract duration, and he was released at the end of 2008. In 2015 whilst assistant manager of Stevenage, Watson alongside Stevenage manager Teddy Sheringham registered as players.
Coaching career
After his release from a playing contract at Luton, Watson was given the position of first-team coach by Luton manager Mick Harford on 14 January 2009. After Harford's departure on 1 October 2009, Watson continued in his coaching capacity under new boss Richard Money until May 2010, when he left the club. Following the departure of Aidy Boothroyd from Colchester United to take the manager's job at Coventry City on 20 May 2010, Watson expressed an interest in taking up the vacant managerial position at his former club. In May 2015 he was appointed manager of Maldon & Tiptree However, Watson left the club after only eleven days to take up the position of assistant manager to Teddy Sheringham at Stevenage. He left his position in February after Teddy Sheringham's departure. From July 2015 to November 2015, he worked at the academy of Colchester United. In August 2016, Watson was appointed Assistant Manager at Eastleigh. In January 2017 he was appointed to the same position at Whitehawk but left the club after just two games, following a change of manager. In March 2017 he was appointed manager of Bishop's Stortford. He left the club at the end of the 2017–18 season. On 28 June 2018, Watson was appointed assistant manager of Hungerford Town. He left the club on 2 October to join Ebbsfleet United as a first-team coach. However, only eight days later, he was appointed caretaker after manager Gary Hill's departure. After a three-game unbeaten run the club confirmed, that Watson had been appointed to the manager's job on a permanent basis. Watson left the club at the end of his contract in May 2020.