On March 8, he was assigned to the Mets minor league camp. After rehabilitating from surgery, Humber resumed pitching with St. Lucie in 2006, posting a 2.37 ERA in seven starts. He compiled a 3–1 win–loss record. On July 31, 2006, a year after his surgery, Humber was once again promoted to Binghamton, where he was 2–2 with a 2.88 ERA. He was an early September call-up when the Major League rosters expanded on September 1. However, Humber did not make his Major League Baseball debut until September 24, 2006. He made two appearances for the Mets as a relief pitcher, pitching two innings. However, Humber was unable to obtain his pre-surgery velocity. That fall, he began play in the Arizona Fall League but his participation was discontinued when he endured shoulder tendinitis.