Butler started his career at Scunthorpe United. He made his debut for the Iron, then in the Third Division, on 20 September 2003 as a 34th-minute substitute in a 1–1 draw with Leyton Orient at Brisbane Road. His full debut came three days later, a 2–3 defeat to Burnley at Glanford Park in the third round of the 2003–04 League Cup. Midway through the season Butler signed a four-year contract.

On 7 February 2004 he scored his first goal in a 2–2 home draw with Doncaster Rovers. He made a total of 42 appearances, scoring two goals in the 2003–04 season. The following season he scored ten goals in 37 league games as Scunthorpe finished second in League Two and were promoted to League One. His goal tally that season included scoring twice in a 3–2 home win over Lincoln City on 21 August 2004 and two goals in a 3–1 victory over Rushden & Diamonds at Nene Park on 18 December. He suffered a serious injury in early 2005 before returning to action later in the season. At the end of the season he won four different honours at the club’s annual awards.

The 2005–06 season saw Butler suffer a string of injuries. On 14 January 2006 he was injured in a 1–1 draw with Bristol City at Ashton Gate and was ruled out for the rest of the season.

In the 2007–08 season Butler made 36 league appearances, scoring two goals as the Iron finished 23rd in the Championship and were relegated back to League One. In May 2008 he appeared on Soccer AM’s Crossbar Challenge on Sky Sports 1 dressed as Wonder Woman. Butler left Scunthorpe in June 2008, turning down a new three-year contract offer, so he could move to a club that would be more suitable for his family needs. In six years with the club, Butler made a total of 153 appearances scoring 13 times, playing for them in all three divisions of The Football League.

On 2 July 2008 Butler joined League One club Huddersfield Town on a three-year deal. Along with five other players, he made his Huddersfield debut in a 1–1 draw with Stockport County at the Galpharm Stadium on 9 August 2008. His first goal came in a 3–2 home win over Crewe Alexandra on 1 November 2008. He made a total of 45 appearances in the 2008–09 season, scoring four goals. Butler began the 2009–10 season as a first team regular. However, Terriers manager Lee Clark started using Peter Clarke and Nathan Clarke as the club’s regular centre back pairing.

On 7 January 2010, after not making an appearance for two months, Butler joined Championship side Blackpool on loan until the end of the season. On the move up a division Butler said, “I’m really happy with the move. It’s a weird one because I’ve gone a step up, but it’s something I’m hoping to thrive on. It looks a good club and I’m happy to be here. Hopefully I can play as many games as I can and help this club where it wants to go, which is the Premiership I suppose.” He made his debut two days later in a 1–1 draw with Cardiff City at the Cardiff City Stadium.

After helping Blackpool reach the Premier League, Butler returned to the Galpharm, but had the remainder of his contract paid up on 23 June 2010. In October 2010 Butler joined Rochdale on a trial basis but failed to agree a contract.

On 12 November 2010, Butler joined Football League One side Walsall on a contract until the end of the season. Butler was signed by Chris Hutchings, who was sacked on 4 January 2011—the day after a 4–1 defeat to Peterborough United—following a run of poor League form since the beginning of the season, which had seen Walsall sink to the bottom of League One. He was appointed captain after Dean Smith, the club’s Head of Youth, took charge of the first team, and scored his first goal for Walsall in a 3–3 draw against fellow strugglers Tranmere Rovers on 8 January 2011. An impressive second half of the season earned Butler Walsall’s Player of the Season and Players’ Player of the Season awards. On 13 May 2011, Butler signed a new two-year contract, keeping him at the club until June 2013. In early May 2014, Butler was offered a new contract with Walsall, however, he rejected new terms with Walsall on 22 May; he made 176 appearances in total for the West Midlands club.

On 5 June 2014, Butler signed a two-year deal with Sheffield United on a free transfer after rejecting the offer of a new deal with Walsall. On 13 August 2014, Butler scored on his début against Mansfield Town in the League Cup. On 11 September 2014, Butler was loaned to former club Walsall on a one-month loan deal after finding first team football hard to come by at United. Butler returned to Sheffield United on 20 October 2014.

On 23 October 2014, Butler went out on loan to home-town club Doncaster Rovers until January 2015. On 6 January 2015, Butler signed permanently for Doncaster Rovers for an undisclosed fee on a two-and-a-half-year deal, having made 13 appearances during his loan spell.

In 2017, Butler became a member of the management committee of the PFA.

On 11 September 2020 he was signed by Rovers on a contract until January 2021.