The Philadelphia Phillies chose Cherry in the 10th round (290th overall) of the 2001 MLB draft, but he did not sign at the time.[3] The next year, the Chicago Cubs selected him in the 14th round (423rd overall) of the 2002 MLB draft, and he signed with them.[4] He was a starter for his first three minor league seasons (2003–2005). Cherry's 2005 season ended after only three appearances for the West Tenn Diamond Jaxx of the Double-A Southern League, after which he had Tommy John surgery. When he returned to West Tenn in 2006, Cherry became a full-time reliever. He had a middle finger injury to his pitching hand in mid-July which also required surgery.[5]
Cherry made his major league debut with the Cubs on April 23, 2007, against the Milwaukee Brewers, He allowed a game-winning home run in the 12th inning to Brewers first baseman Prince Fielder, and suffered the loss.[6] Cherry earned his first big league win on May 1 against the Pittsburgh Pirates.[7]
Baltimore Orioles
In August 2007, the Cubs traded Cherry and third baseman Scott Moore to the Orioles for starting pitcher Steve Trachsel.[8] Cherry began 2008 on the 15-day disabled list with a shoulder strain.[9] As of May 20, he was on rehab assignment to the Triple-A Norfolk Tides. He was the last visiting pitcher ever at the original Yankee Stadium while a member of the Orioles on September 21, 2008.[10]
New York Mets
In December 2008, Cherry was selected by the New York Mets in the 2008 Rule 5 draft. He was released by the Mets on March 17, 2009, after the Orioles declined to take him back.[11]
Boston Red Sox
On March 24, 2009, Cherry signed a minor league contract with the Boston Red Sox.[12] He was released on August 18, 2009.
San Diego Padres
On August 21, 2009, Cherry signed a minor league contract with the San Diego Padres.[13] He was granted free agency on November 9, 2009.