Parnell worked as a starter for the minor league teams in the Mets organization, pitching for the Brooklyn Cyclones, St. Lucie Mets, Binghamton Mets, and New Orleans Zephyrs. In three different leagues, Parnell has been named a mid-season All-Star. He earned the honor in the New York-Penn League in 2005, the Florida State League in 2007, and the Eastern League in 2008. Despite having a poor record since being promoted to the Triple-A New Orleans Zephyrs, Parnell was rewarded with a call-up to the New York Mets on September 1, 2008. Parnell got his first win May 8th against the Pirates, he pitched a scoreless 8th inning.