Wells was drafted by the Chicago Cubs in the 38th round (1,143rd overall) of the 2002 MLB draft as a catcher. He spent his career in the Chicago Cubs farm system from 2003 to 2007 before being claimed in the Rule 5 Draft by the Toronto Blue Jays before the 2008 season. Wells made the opening day roster and made his debut on April 5, 2008, against the Boston Red Sox and pitched a scoreless inning. It was his only appearance for the Blue Jays because he was designated for assignment on April 9, 2008. Wells was returned to the Cubs organization on April 16, and was assigned to the Triple-A Iowa Cubs. On September 9, 2008, the Cubs placed Jon Lieber on the 60-day DL and called up Wells to replace him on the roster. After spring training in 2009, he was returned to the Iowa Cubs. Wells was called up to the Cubs active roster on May 5, 2009 in place of the injured Carlos Zambrano. He made his first start on May 8 against the Milwaukee Brewers and struck out five batters in five scoreless innings, but despite leaving the game with a 2–0 lead, the Cubs' bullpen gave up three runs and eventually lost 3–2. Wells got his first Major League win on June 21, 2009 in a 6–2 win over a struggling and injury plagued Cleveland Indians. On July 29, he became the first Cub rookie pitcher to win seven games since Kerry Wood did it in 1998, when he threw eight shutout innings in a 12–0 Cubs win over the last place Astros.
Wells was designated for assignment by the Cubs on June 27, 2012. At the time, he was 1–2 with a 5.34 ERA in 12 games (four starts). On October 6, 2012, Wells elected free agency.
On December 6, 2012, Wells signed a minor league contract with the Texas Rangers organization. On April 30, he announced his retirement.

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