Riley ran track at Muleshoe High School in Muleshoe, a town in West Texas. He began his high school career at defensive end and made the move to quarterback for his junior and senior seasons. Riley played quarterback at Texas Tech University as a walk-on in 2002, behind senior starter and future Texas Tech coach Kliff Kingsbury and back-up B. J. Symons. After a year, he became a student assistant to Mike Leach, gradually progressing to graduate assistant and then to receivers coach. Following his departure from Texas Tech after the firing of Leach, Lincoln went on to serve five seasons as offensive coordinator at East Carolina University under Ruffin McNeill.