During the start of his 2013 outdoor season, he DNFed in the 5000 m at the Oxy High Performance Meet, but he got second in the 1500 m at this same meet in 3:36.98. He was sixth in the Prefontaine Classic 5000 m. At the 2013 USATF Championships, he won his fifth consecutive US 10k Outdoor title, in a time of 28:47.32. His teammate, Dathan Ritzenhein, led the last four laps or so, but he was to be outkicked by Rupp in the end. He was also the runner up in the 5000 m to Bernard Lagat, much like last year but with the opposite outcome. This qualified Rupp for two events at the IAAF World Championships in Moscow. He raced the 5000 m at the Monaco Diamond League Meet, where there were rumors of him and Lagat going after the American record in that race. However, Rupp came out on top because Lagat DNFed, no American record was broken that day. At the London Diamond League meet, his last race before Moscow, he raced in the Emsley Carr Mile, where he was the top American in an international field, even though he is a 10k specialist. He set an outdoor personal best of 3:52.11, beating out a field that included his 1500 m specialist teammate Matthew Centrowitz.