Harrington was a member of the U-17 Residency Program at the Bradenton Academy and while there played for the US at the 2003 FIFA U-17 World Championship in Finland in which the team reached the quarterfinals. Two years later Harrington represented America at the 2005 FIFA World Youth Championship in Holland. He attended the University of North Carolina, Chapel Hill where he played on the men's soccer team from 2003 to 2006. During the collegiate off season, he also played for the Raleigh CASL Elite of the fourth division Premier Development League. In 2007, the Kansas City Wizards of Major League Soccer selected Harrington in the first round (third overall) of the SuperDraft.