The team was led by third-year head coach Paul Johnson. The Midshipmen finished the regular season with a 9–2 record, the first time since the 1963 college football season that Navy had won nine or more games in a season. Wins over Army and the Air Force Falcons secured Navy's second consecutive Commander-in-Chief's Trophy. Navy secured a berth in the 2004 Emerald Bowl when the Pacific-10 Conference did not have enough teams to fill its bowl obligations. The other tie-in was with the Mountain West Conference (MWC), and the Midshipmen ended up playing the New Mexico Lobos. They won the game with a score of 34–19, finishing with a 14-minute, 26-play drive that set the record for the longest drive in a college football game. The win gave the Midshipmen a final record of 10–2, the first time since the 1905 season that the Midshipmen finished with ten or more wins.