Due to several incidents during the 2003 NFL season, officials are authorized to penalize excessive celebration. The 15-yard unsportsmanlike conduct penalty will be marked off from the spot at the end of the previous play or, after a score, on the ensuing kickoff. If the infraction is ruled flagrant by the officials, the player(s) are ejected.
Due to several instances in one game (NE vs. IND) during the 2003–04 playoffs, officials are instructed to strictly enforce illegal contact, pass interference, and defensive holding.
Timeouts can be called by head coaches.
In addition to the numbers 80–89, wide receivers will now be allowed to use numbers 10–19.
A punt or missed field goal that is untouched by the receiving team is immediately dead once it touches either the end zone or any member of the kicking team in the end zone. Previously, a punt or missed field goal that lands in the end zone before being controlled by the kicking team could be picked up by a member of the receiving team and immediately run the other way.
Teams will be awarded a third instant replay challenge if their first two are successful. Previously, teams were only limited to two regardless of what occurred during the game.
The one-bar facemask was officially outlawed. The few remaining players who still used the one-bar facemask at the time were allowed to continue to use the style until they left the league under a grandfather clause.
Midway through the season, Johnny Grier suffered a leg injury that forced him to retire. He was permanently replaced by the back judge on his crew, Scott Green, who had previous experience as a referee in NFL Europe.
Within each conference, the four division winners and the two wild card teams (the top two non-division winners with the best overall regular season records) qualified for the playoffs. The four division winners are seeded 1 through 4 based on their overall won-lost-tied record, and the wild card teams are seeded 5 and 6. The NFL does not use a fixed bracket playoff system, and there are no restrictions regarding teams from the same division matching up in any round. In the first round, dubbed the wild-card playoffs or wild-card weekend, the third-seeded division winner hosts the sixth seed wild card, and the fourth seed hosts the fifth. The 1 and 2 seeds from each conference then receive a bye in the first round. In the second round, the divisional playoffs, the number 1 seed hosts the worst surviving seed from the first round (seed 4, 5 or 6), while the number 2 seed will play the other team (seed 3, 4 or 5). The two surviving teams from each conference's divisional playoff games then meet in the respective AFC and NFC Conference Championship games, hosted by the higher seed. Although the Super Bowl, the fourth and final round of the playoffs, is played at a neutral site, the designated home team is based on an annual rotation by conference.
The Colts led the NFL with 522 points scored. The Colts tallied more points in the first half of each of their games of the 2004 NFL season (277 points) than seven other NFL teams managed in the entire season. Despite throwing for 49 touchdown passes, Peyton Manning attempted fewer than 500 passes for the first time in his NFL career. The San Francisco 49ers record 420 consecutive scoring games that had started in Week 5 of the 1977 season ended in Week 2 of the season.