After the brief stint in spring training, the Mets assigned Humber to start his professional career with the St. Lucie Mets of the Class-A Advanced Florida State League, where, in fourteen starts, he posted a 2–6 win–loss record and a 4.99 ERA. Humber was then promoted to the Class-AA Binghamton Mets of the Eastern League. In one start, Humber gave up three earned runs in four innings. Humber left the game early due to elbow pain caused by bone spurs, which required ulnar collateral ligament reconstruction (more commonly known as Tommy John surgery) to repair a torn ligament in his elbow. The surgery was performed by Dr. James Andrews of the American Sports Medicine Institute. His Rice pitching teammates Townsend (Tommy John surgery) and Niemann (arthroscopic shoulder surgery) also endured major surgeries that year. Rice coach Graham, who also coached MLB starters such as Roger Clemens and Andy Pettitte in college, shied away from any blame, noting that all three missed out on fall league play by holding out. In spite of his arm surgery, Humber was named the 20th-best prospect in the Florida State League by "Baseball America", which ranked him as the fifth-best prospect in the Mets organization following the season.