On October 2, 1998, Stokes was signed as an amateur free agent by the Tampa Bay Devil Rays.[2] He spent his first professional season with the Princeton Devil Raysin1999. While with Princeton, he led the Appalachian League in games finished with 35. He pitched for Charleston (Single-A) in 2000, allowing one home run in 70.1 innings pitched. Stokes pitched his first complete game at Mudville on June 23, 2001, but lost the game. He played for Bakersfield during the 2002 season, leading the team in wins (10) and strikeouts (154). He threw his first professional shutout on July 14 against San Jose. Stokes started ten games for Orlando (Double-A) before undergoing Tommy John surgeryin2003, resulting in his missing the entire 2004 season. In 2005, Stokes pitched for both Visalia (Single-A) and Montgomery (Double-A). A hamstring injury sidelined him for the month of July. He was recalled from Durham (Triple-A) on September 2, 2005.
Stokes made his major league debut on September 3, 2006. In 2007, Brian's 59 appearances were fourth among American League rookies.[3]
On November 28, 2007, Stokes was sent from Tampa Bay to the New York Mets for cash considerations and was added to the Mets' 40-man roster.[3] During spring training on the last day, he was designated for assignment. He started the season with the Mets Triple-A affiliate, the New Orleans Zephyrs. He was called up to the Mets on August 9, 2008, to start in place of injured starting pitcher, John Maine.[4]
On August 1, 2011, Stokes signed a minor league contract with the Arizona Diamondbacks, he was assigned to the Triple-A Reno Aces. He became a free agent following the season on November 2.
