Jones graduated in 2000 from Scotch Plains-Fanwood High School, where he played running back and defensive back.Malool, Amanda. "District honors NFL's Nate Jones '00; retires #22", The Fanscotian, November 27, 2012. Accessed November 13, 2018. "In June, 2000, Nate Jones was graduating Scotch Plains-Fanwood High School. In June, 2012, his jersey was being retired to mark his outstanding academic and athletic career; the first jersey in the football program at Scotch Plains-Fanwood High School." As a senior, he was a first-team All-state selection and the Offensive Player of the Year in Union County, after recording 2,474 rushing yards, 33 rushing touchdowns, 10 receptions, 227 receiving yards and 3 receiving touchdowns.
