After the 2005 season, Long landed his first head coaching position when he was hired as the 16th head football coach at San Diego State University. Long had a record of 9–27 in three seasons as SDSU's head coach. On November 23, 2008, college president Stephen Weber announced that Athletic Director Jeff Schemmel had dismissed Long prior to the final game of the season. Coach Long finished his third season only winning 2 out of 12 games, including the one conference win on his final night. San Diego State finished the 2008 season with a 2–10 record, the first and only ten-loss season in school history. Long also had the distinction of having his team lose two games to Division I-AA Cal Poly San Luis Obispo (in his first and third seasons with the Aztecs, respectively).