Rupp's 2009 track season was a resounding success. Indoors, he joined the sub-4:00 club for the mile on March 7 by running 3:57.86 at the Husky Last Chance Qualifier Meet in Seattle, WA. On February 13, 2009, he broke the American indoor 5000 m record with a time of 13:18.12 at the Tyson Invitational in Fayetteville, Arkansas. At the NCAA indoor nationals, he won an unprecedented triple in the 5000 m (13:41.45), the distance medley relay (running a 3:57.07 1600 m anchor leg only 90 minutes after his 5000 victory), and the 3000 m (7:48.94, the next day). This triple victory helped Oregon win its first-ever indoor national team title.