Having begun his professional career with Hull City in 2006, Atkinson spent time on loan with Port Vale, Mansfield Town, Rochdale (twice), Rotherham United and Plymouth Argyle. He was promoted out of League Two with Rochdale in 2009–10. He signed with Bradford City in July 2012, and played in the 2013 League Cup final defeat and the 2013 League Two play-off final victory. He signed with Southend United in July 2013, and helped the club to win the 2015 League Two play-off final. He signed with Mansfield Town in May 2017. He signed a short-term deal with Port Vale in October 2019, remaining at the club until the end of the 2019–20 season. He signed with Southend United in August 2021 after spending the curtailed 2020–21 season with Alfreton Town.