Shafer was hired by Syracuse University head football coach Doug Marrone in 2009. He was hired as the defensive coordinator for a team that allowed 32.7 points per game in the 2008 season. The defense went from being 101st in the country to the top 20 under Shafer. Under Shafer, Syracuse's defense ranked 7th in the nation in 2010 in total defense (from 37th), 12th in the nation in first downs allowed (from 27th), 10th in pass defense (from 85th), 14th in pass efficiency defense (from (113th), and 13th in scoring defense (from 81st). While at Syracuse, he coached 2012 1st round draft pick Chandler Jones, who was the highest draft pick from Syracuse since Dwight Freeney in 2002. Shafer was officially named the head coach of the Orange on January 9, 2013 after Doug Marrone left to become the head coach of the Buffalo Bills.