After playing two years of college soccer at Clemson University, Holden signed with English club Sunderland in early 2005. On March 12, Holden was attacked outside a bar in Newcastle because he was a Sunderland player, leaving him with a fractured left eye socket, which prevented him from training with the club for two months. When Holden resumed training, he suffered an ankle injury that ruled him out for the rest of the season. Holden was released after his six-month stay having never played for Sunderland's first team.
Stuart Holden playing for Houston Dynamo in 2009.
Holden returned to the United States to play in Major League Soccer with the Houston Dynamo for the 2006 season. He made his MLS debut on May 27, 2006, and scored his first professional goal on July 22, 2006, in a 1–1 home draw against New England. He appeared thirteen times in the 2006 regular season and twice as a substitute in Houston's run to the MLS Cup 2006 championship. In the championship penalty shootout, Holden took the Dynamo's second shot and scored to the top right corner.
Holden's playing time increased in the 2007 season. He mostly started on the left wing when teammate Brad Davis went down with injury. In July, Holden scored goals on consecutive Thursday night games and added three assists in league play and another in SuperLiga play, as of July 25. Holden was awarded the US Soccer Humanitarian of the Year award in 2008.
Having spent several weeks training in England following the end of the 2009 Major League Soccer season, Holden officially joined Premier League side Bolton Wanderers on January 25, 2010. He made his debut on February 24, 2010 in a 4–0 defeat against Tottenham Hotspur in the FA Cup, starting and playing the full ninety minutes. He made his first league appearance on February 27, 2010, playing the full 90 minutes in a 1–0 victory over Wolverhampton Wanderers. On September 30, 2010, he signed a new contract at Bolton, which would keep him at the club until 2013. He scored his first goal for Bolton away to Wolverhampton Wanderers on November 13, 2010.
Stuart Holden and Nicolas Anelka during a match in the Premier League.
In the 2010–11 season, Holden helped Bolton reach seventh place in the Premier League and to the FA Cup Semi-finals. However, his season was cut short on March 19 after he suffered a knee injury against Manchester United at Old Trafford when going into a tackle with Jonny Evans. Evans' studs caught Holden in the left knee, leaving a gash that required twenty six stitches and a fracture of the femur near the knee joint, which ruled him out for a minimum of six months. Despite missing the final two months of the season, Holden was still voted the 2011 Bolton Wanderers Player of the Year. Without Holden, Bolton finished the season in fourteenth position.
On September 20, 2011, after six months out, Holden started and played the full ninety minutes against Aston Villa in the third round of the League Cup, but was then initially ruled out for a further six weeks as the club brought forward a routine follow up procedure. However, the procedure revealed cartilage damage, meaning Holden would be out for a further six months, missing the rest of the season. Later on in the season, Bolton Wanderers were relegated to the Championship after 11 years in the Premier League.
On June 22, 2012, Holden announced via his Twitter account that he was due to switch to the number 22 shirt after it had been vacated by Jussi Jääskeläinen. This was confirmed by the club when they released their squad numbers on July 5.