The following March, Rupp capped his indoor season by placing third in the 5000 m and fourth in the 3000 m at the 2007 NCAA Men's Indoor Track and Field Championship. He began his outdoor season by running a 28:35 10,000 m at Stanford. During the race, he caused some controversy by frequently slowing down to wait for another athlete. On April 20, 2007, Rupp made a huge comeback in the last 200 meters of a 5000 m race to edge out Chris Solinsky, improving personal best to 13:30. On April 29, 2007, Rupp defeated a stellar field to win the men's 10,000 m at the Payton Jordan Cardinal Invitational at Stanford. Rupp's time of 27:33.48 set an American-born NCAA Collegiate Record for the event and also gave him the seventh-fastest time in U.S. history. Two weeks later, Rupp won the 10,000 and 5000 m at the Pac-10 conference meet and helped Oregon to the team title. As in his freshman year, he went on to finish second in the 10,000 m at the NCAA track and field championships.