As with the previous three seasons, the AFL had 8 teams, split into two divisions. Every team played two games against the others for a total of 14 games, and the division winners met in the AFL championship game. If there was a tie in the standings at the top of either division, a one-game playoff was held to determine the division winner. San Diego led the Western Division for the entire season, with the Oakland Raiders following one game behind from Week Eight onward. The Raiders had started at 2–0, then lost four straight, then began a winning streak. Starting from a 2–4 handicap was insurmountable, and although Oakland beat San Diego twice (34–33 on October 27, and 41–27 on December 8), they were unable to catch up.
The Eastern race changed in Week Seven, after the Jets lost to Oakland, 49–26, and the Patriots and Houston Oilers tied at 4–3–0 for the lead. Houston, winner of the first three Eastern titles, pulled ahead the next week, and Boston beat them 45–3 the week after that; the next week, Boston lost 7–6 to San Diego, while Houston beat the Jets 31–27 to pull ahead again. Two weeks later (Week Twelve), San Diego beat Houston 27–0, while Boston led again after a 17–7 win over the Buffalo Bills. In Week Thirteen, Boston was at 7–5–1, and Buffalo and Houston right behind. In the final week, spoiler San Diego took out Houston, 20–14. Buffalo won 19–10 over the Jets, while Boston lost 35–3 at Kansas City, giving the Bills and Pats records of 7–6–1 and forcing a one-game playoff, for a spot in the AFL Championship game.
The season schedule itself was pushed back a week from what was originally planned, owing to the assassination of President Kennedy, which resulted in the AFL moving games from that weekend (i.e., the weekend of November 23–24) to the weekend of December 21–22. Since only three games had been scheduled, with Boston and Buffalo both having a bye, it meant that the Patriots and Bills finished their regular schedule on Saturday, December 14, a week before the league's other six teams did. Consequently, the Patriots and Bills could have played their tiebreaker playoff on December 22, potentially leaving the AFL Championship Game for the next weekend (the originally scheduled date), since they knew after games of December 15 that they and they alone had tied for the division title. However, the Western Division race had not yet been decided and Chargers and Raiders owners Barron Hilton and Al Davis respectively objected to playing the Eastern playoff "early" on the grounds that it would have given the Eastern winner an unfair advantage in terms of rest in case the Chargers and Raiders also had to play a tiebreaker. The Chargers won their last game and with it won the West outright, nevertheless the Bills-Patriots Eastern Division playoff was not played until after the following week on Saturday, December 28 (the day before the Chicago-New York NFL Championship Game). This meant that the Boston-San Diego championship game was not played until January 5, 1964. Thus was held the second professional playoff game ever held in January (with the AFL's first ever title playoff on January 1, 1961, being the only time before then that that had occurred). As it happened, the Patriots-Chargers playoff was also latest date on which a non-Super Bowl playoff game was ever held, and it retained that record until the AFC and NFC Championship Games of January 7, 1979. No 14-game season ever ended later.