Born in Gateshead, Nelson started his playing career as a semi-professional, playing for non-League teams such as Spennymoor United, Leek Town and Bishop Auckland. Nelson's performances attracted the attention of league clubs who sent scouts to watch him. Nelson was given a trial at Hartlepool but he was not offered a contract by the then Hartlepool manager Chris Turner. However Nelson was offered a contract at Bury by manager Andy Preece after Bury scout Peter Ward convinced him to give Nelson a chance.
Once Nelson had settled down to professional football, he gradually became a first team regular and during his first full season at Bury he managed to play 31 of the clubs 46 league matches, scoring 2 goals in the process. Nelson formed a defensive partnership with Danny Swailes. However, during the season Nelson suffered what he described as ‘‘the worst injury of his career’’ after suffering a collapsed lung and several cracked ribs after a collision during Bury's match against Wigan Athletic. Nelson had to have a drain inserted into his chest for several days while he was hospitalised. The injury threatened to keep him sidelined for three months but remarkably Nelson was able to resume training less than three weeks later.
Despite being dropped early on, Nelson's second season turned out to be even more successful as he played in 40 of Bury's 46 matches, scoring 5 goals. Nelson was made club captain and his performances earned him the respect of the club's players and fans. During that season, Bury manager Andy Preece hailed Nelson as "the best centre-half in Division Three". However, Bury failed to gain promotion to League 1 as they missed out during the play-offs and Nelson was offered the chance to play in a higher division by several League 1 clubs.
The following season, Nelson joined Hartlepool United on the same day that Neale Cooper was appointed manager for a fee of around £70,000. Nelson was seen as natural replacement for Graeme Lee who had joined Sheffield Wednesday. Nelson started strongly for Hartlepool and scored the winner from 30 yards during his debut in Hartlepool's 4–3 win over Peterborough. This goal almost earned him another award as it was on the shortlist for Hartlepool's Goal of the Season. He was also voted September's Player of the Month on the official Hartlepool website. Nelson began to form a strong partnership with Chris Westwood and the pair played together for the majority of Hartlepool's games. Nelson went on to play in 40 of Hartlepool's league matches and played in both legs of Hartlepool's play-off semi-final match against Bristol City. Nelson was in contention for Hartlepool's Fans and Players’ Player of the season but he missed out to Jim Provett on both occasions.
However Nelson failed to maintain this through to the 2004–05 season and he handed in a transfer request. His agent claimed that he’d been "promised" a better deal. This triggered a feud with Hartlepool chairman Ken Hodcroft who criticised Nelson and his agent. Nelson was missing in several of Hartlepool's matches and was rumoured to be signing for Hull City for a fee of around £100,000. However Nelson withdrew his transfer request and was reinstalled into the starting line-up. His performances earned him an improved contract and he was offered a new three-year contract that would tie him to the club until 2008.
Nelson's third season of the club saw him receiving his first red card for Hartlepool after he retaliated and elbowed Jack Lester during Hartlepool's defeat to Nottingham Forest. He was the favoured central defender alongside Ben Clark during the 2006–07 campaign, playing a major part in the 18 game unbeaten run along with Dimitrios Konstantopoulos in goal. The season also saw him take the captain's armband in the absence on Michael Barron.
Nelson was named in the PFA League Two Team of the Year for the 2006–07 season.
In June 2009, Nelson agreed to join Norwich City, who had just been relegated to League One, on a two-year deal once his contract at Hartlepool expired at the end of the month. He made his debut in the 7–1 opening-day thrashing at the hands of Colchester, and did not play for the first team again until the game against his former club Hartlepool later in August, in which he scored a magnificent overhead kick. It was his first goal for Norwich and put the Canaries on course for a 2–0 win at Victoria Park. Nelson established himself as a regular starter following an injury to teammate Jens Berthel Askou in December. He subsequently formed a strong central defensive partnership with Gary Doherty as Norwich surged up the League One table, overhauling runaway leaders Leeds United in the process. On 17 April 2010, he scored the only goal in a 1–0 victory at Charlton Athletic which secured Norwich's return to the Championship at the first attempt. Nelson's scored his third goal for Norwich in a 2–0 win over Gillingham. In his second season, Nelson scored his fourth goal against Watford in a 3–2 loss in Norwich City's first match of the season. Nelson scored his fifth and last goal for Norwich against Sheffield United in a 4–2 win. Nelson remained in the first team for Norwich City until he suffered a foot injury. Following his return from injury, Nelson was targeting the first team but was deemed surplus to requirements by Canaries boss Paul Lambert as Lambert favoured Elliott Ward and Leon Barnett as their first choice centre back. Nelson is held in very high esteem by Norwich City fans for his performances during the successful League One campaign. He received a standing ovation from Carrow Road on his return with new club Scunthorpe United.
He left the Canaries on deadline day in January 2011 for an undisclosed fee, joining Scunthorpe United, just an hour from the deadline. Nelson made his debut for Scunthorpe United in a disastrous 5–1 defeat to Hull City. At the end of the season, Scunthorpe were relegated to League One. Nelson scored his first goal for Scunthorpe in a 1–1 draw against Wycombe Wanderers. Scunthorpe's poor form continued and at the end of 2011 the club was just above the relegation zone to League Two. In January 2012, Nelson was strongly linked with move away from Scunthorpe following a restructuring programme at the club.
On 14 January 2012, Nelson signed for Scottish Premier League side Kilmarnock, a two-and-a-half-year contract. After the move, Manager Kenny Shiels described new signing Nelson as 'quality' and expected Nelson will be good asset in the second half of the season. Shortly joining, Nelson revealed that then Norwich City manager Paul Lambert made a recommendation of Nelson joining Kilmarnock. Nelson had to wait until on 4 February 2012 when he made his debut, playing in the central defence, in a 1–1 draw against Dunfermline Athletic. Then on 18 March, he played in the 2012 Scottish League Cup Final which Kilmarnock won after beating Celtic 1–0. A week after the Scottish League Cup Final, Nelson scored his first goal for the club in a 4–3 thriller victory over Inverness Caledonian Thistle The next season, Nelson continued to retain his first team place until he left and start his new season when he scored his first goal in the second round of Scottish League Cup, in a 2–1 loss against Stenhousemuir and he soon scored his second goal for the club in a 2–1 loss against St Johnstone on 24 November 2012.
On 15 January 2013, Nelson agreed to join Bradford City on an 18-month deal for an undisclosed fee. Thirty days later, on 15 February 2013, when asked why Nelson was sold, Shiels then explained his decision selling Nelson, that he wanted to be close with his children and described his departure as a "big loss". He made his debut on 2 February, in a 2–2 draw away to Fleetwood Town. Nelson was an unused substitute as Bradford won promotion to League One by winning the 2013 Football League Two play-off Final.
On 1 August 2013 Nelson signed a two-year deal with Scottish Premiership side Hibernian, moving from Bradford City for a nominal transfer fee. He had then left the club after agreeing mutual termination of his contract.
On 26 August 2014 Nelson signed a one-year contract with League Two side Cambridge United shortly after agreeing mutual termination with his previous club Hibernian. At the end of the 2014–15 season the club did not offer him a new deal when his contract expired.
Nelson joined Barnet on trial in 2015–16 pre-season, and signed a one-year deal on 3 August.As of 6 May 2017
Hartlepool UnitedFootball League Two runners-up: 2006–07
Norwich CityFootball League One: 2009–10
KilmarnockScottish League Cup: 2011–12
IndividualBury Player of the Year: 2002–03
PFA League Two Team of the Year: 2007