Atkinson made his first appearance as an official in the Football League as an assistant referee in 1995. Since he was promoted to the list of Select Group Referees in 2005 he has refereed a number of notable matches, including the FA Community Shield and the finals of the FA Trophy, Football League Cup, FA Cup and UEFA Europa League.
Atkinson started his refereeing career at the relatively early age of 16 years, as the local team did not have a referee to oversee matches. By 1998, he had been promoted to the Football League's list of assistant referees.
This was followed in 2000 by promotion to the Select Group of assistant referees. By December 2002 he was refereeing Football Conference matches, and also refereed the 2003 FA County Youth Cup final.
At the start of the 2003–04 season, Atkinson joined the national list of referees. He had the distinction of not sending off any player from the field of play between August 2004 and October 2005.
Only two years after his Conference debut, Atkinson was appointed to referee his first Premier League game, taking charge of the Manchester City-Birmingham City fixture on 20 April 2005, cautioning one player and awarding the home side a penalty kick in a 3–0 result.
During the three seasons between 2003 and 2006, Atkinson issued only eight red cards in 102 matches, an average of less than 0.08 per game.
In 2006 Atkinson was appointed to the list of FIFA referees.
The 2009–10 season saw Atkinson referee 48 matches in English football, his highest tally of appointments in one season to date.
In September 2010, Atkinson was handed a one-week demotion to the role of fourth official after a time-keeping dispute with Everton manager David Moyes. Everton had scored two injury-time goals to make the score 3–3 against Manchester United, but Atkinson then blew his final whistle while Everton were midway through an attack with a chance of a winner.
Atkinson refereed the 2006 FA Community Shield match at the Millennium Stadium in Cardiff. Liverpool defeated Chelsea 2–1, with Atkinson issuing four yellow cards during the course of the game.
Atkinson was appointed to referee the 2008 FA Trophy Final at Wembley Stadium, which was contested between Ebbsfleet United and Torquay United.
Atkinson was appointed to officiate the 2011 FA Cup Final. Manchester City defeated Stoke City 1–0; Atkinson issued two yellow cards to two Stoke players during the match.
Atkinson refereed the 2014 Football League Cup Final between Manchester City and Sunderland. City won the match 3–1 and Atkinson cautioned two players, both late in the second half.
On 13 October 2007, Atkinson refereed a group C qualifier for Euro 2008 between Moldova and Turkey. The game in the Moldovan capital Chişinău ended a 1–1 draw, with the referee showing two yellow cards.
The 2008–09 season was the first that Atkinson took charge of UEFA Champions League games. That season he refereed four matches, including FC Zürich against Real Madrid and Inter Milan versus Dynamo Kiev. In 2010 Atkinson was fourth official to Howard Webb for the Champions League final in Madrid. He issued his first Champions League red card on 5 April 2011, to Cristian Chivu of Inter Milan as they lost 5–2 at home to Schalke.
Atkinson officiated multiple matches during 2010 FIFA World Cup Qualification, including the UEFA group 4 qualifying game between Germany and Finland in Hamburg on 14 October 2009 which ended 1–1. One month later, he officiated Portugal's 1–0 qualifying win over Bosnia and Herzegovina.
He officiated at Euro 2012 as an additional assistant referee in a team with referee Howard Webb.
The referee abandoned a Euro 2016 qualifying match in Belgrade between Serbia and Albania on 14 October 2014 when violence on the pitch and crowd disturbances broke out after a quadcopter was flown over the pitch bearing a flag of Greater Albania.
Atkinson refereed a UEFA European Championship game for the first time on 12 June 2016 – a Euro 2016 group match between Germany and Ukraine.
Statistics for all competitions. No records are available prior to 2002/03.