Clippard was drafted in the 9th round of the 2003 MLB Draft by the New York Yankees out of J. W. Mitchell High School. He played ball for the Central Florida Renegades Connie Mack team in Florida when he was drafted. From 2003-2006, in the minor leagues, he averaged 7.5 hits, 2 walks, and 10 strikeouts per 9 innings for Yankees' farm teams. While playing for the Trenton Thunder in 2006, Clippard threw the franchise's first no-hitter.