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2016: Fifth Super Bowl win

After serving his four-game suspension, Brady made his 2016 season debut on October 9 on the road against the Browns; he completed 28-of-40 passes for 406 yards and three touchdowns in a 33–13 victory to earn AFC Offensive Player of the Week. Brady's outstanding numbers during his first four games following the suspension earned him the AFC Offensive Player of the Month award for October.

In Week 11, Brady recorded four touchdowns and no interceptions in a 30–17 road win against the 49ers. Those four touchdown passes gave him a total of 444 career regular season touchdown passes with one team, breaking Brett Favre's record with the Green Bay Packers. The following week, Brady completed 30-of-50 passes for 286 yards and two touchdowns in a 22–17 road victory against the Jets. The win was also the Patriots' 500th victory (including playoffs) in franchise history. During this victory, Brady also became the fifth quarterback to record 60,000 career regular season passing yards, joining Peyton Manning, Brett Favre, Drew Brees, and Dan Marino. The following week, Brady and the Patriots defeated the Los Angeles Rams by a score of 26–10, giving Brady his record-201st career victory, including playoff games.

With a 16–3 victory over the Broncos, the Patriots clinched an eighth consecutive AFC East title and a seventh consecutive first-round bye in the playoffs, both NFL records. On December 20, 2016, Brady was named to the Pro Bowl for the eighth straight season and 12th time overall. Brady ended the regular season with 28 passing touchdowns and only two interceptions for the regular season, breaking the previous TD:INT ratio record of Nick Foles 's 27:2 figure set in 2013 with the Eagles. Brady was named to the AP All-Pro Second Team. Brady was also ranked first on the NFL Top 100 Players of 2017 as the best player in the league, becoming the first player to be named as #1 twice since the listing began.

Brady and the Patriots began their postseason run in the Divisional Round, hosting the Texans, which held the league's No. 1 total defense. Brady completed 18-of-38 passes for 287 yards, two touchdowns, and two interceptions as the Patriots won 34–16, clinching a record sixth consecutive trip to the AFC Championship Game. In the AFC Championship, the Patriots hosted the Steelers. Brady completed 32-of-42 passes for 384 yards, three touchdowns, and no interceptions in the 36–17 victory. The win gave Brady and Patriots head coach Bill Belichick their record seventh conference title as a quarterback–head coach tandem, and the Patriots an NFL record ninth Super Bowl appearance.

Brady and the Patriots faced the NFC champion Atlanta Falcons, who boasted the league's highest-scoring offense, in Super Bowl LI. Brady threw for 43 completions on 62 attempts for 466 passing yards—all Super Bowl records at the time. Brady also threw for two touchdowns and an interception, which was returned for a touchdown by Robert Alford in the second quarter. After trailing 28–3 midway through the third quarter, Brady and the Patriots scored 25 unanswered points to tie the game at the end of regulation. This resulted in the first overtime in Super Bowl history. After winning the overtime coin toss, Brady led the Patriots down the field to score a touchdown and win the game by a score of 34–28, completing the largest comeback win in both team history and Super Bowl history. With the victory, Brady won his fifth Super Bowl, which set a record for most Super Bowl victories of any quarterback in history and tied defensive player Charles Haley for the most Super Bowl victories for any player. In addition, Brady set another record by winning his fourth Super Bowl MVP award for his clutch performance. On a personal note, this game was also special for Brady because it was the first game this season that his mother had attended in person, after having been previously diagnosed with cancer.