Recovering from the Olympics, Rupp avoided the early 2008 cross country season, running his first race at the Pac-10 Conference Championships, which he won in a course-record 22:55 over 8K. He then repeated as NCAA West Regional champion by running 27:41.24 to win the 10K race. In the 2008 NCAA national cross country championships, Rupp won his first individual NCAA title by outkicking Liberty University's Sam Chelanga in a time of 29:03.8, a new course record on the Terre Haute, IN, site, and leading the Ducks to repeat as NCAA team champions.