The following is an excerpt from Warren Sharp's 2026 Football Preview. In addition to Warren's deep, detailed write-up on all 32 NFL teams, each chapter features page after page of full-color charts, stats, and heatmaps, as well as penalty analysis from Joe Gibbs. Click here for a full FREE chapter from the 2026 Football Preview.
Penalties are an under-discussed aspect of NFL success and failure. Average teams can become playoff contenders with good discipline, and good teams can become great simply by winning the penalty battle.
Let's look at how the San Francisco 49ers performed from a penalty perspective in 2025 and where they can improve in 2026.
San Francisco 49ers 2026 Penalty Outlook: Discipline, Flags & Hidden Edges
The Good
- The 49ers ranked 31st in penalties per game, eclipsed only by the division-rival Rams in this category.
- San Francisco averaged the fewest penalties per game at home in 2025.
- The 49ers averaged the fewest fourth-quarter penalties in 2025.
- The Niners averaged the fewest offensive penalties per game last season.
- San Francisco averaged the third-fewest offensive penalties per game on third-down plays.
- The 49ers averaged the fewest pre-snap penalties per game in 2025.
- The special teams unit was the least penalized in the NFL.
- The Niners had the third-worst net negative penalty yards per game in 2024. They flipped that in 2025, ranking as a top-10 beneficiary in yards per game.
- In raw numbers, the 49ers averaged the fewest penalties per game via the offensive holding and false start penalty combination.
The Bad
- The 49ers ranked second overall for unnecessary roughness penalties.
- The offense averaged just 7.8 yards per beneficial defensive pass interference, compared to a league average of 15.2 yards. Watch this space with the arrival of Mike Evans in San Francisco. Evans has been an integral part of one of the most efficient offenses in this category during his time down in Tampa Bay, and it will be interesting to see if that advantage translates to the same extent in Kyle Shanahan’s system.
Grade: A+
The 49ers’ reliance on a core group of veterans like Trent Williams, Christian McCaffrey, Nick Bosa, and the recently acquired Mike Evans is cause for concern, given the injury history of this franchise over the past few seasons.
If the 49ers lose two or three stars simultaneously again, the roster may not be deep enough to absorb it, especially along the offensive line if Williams were to miss time.
The law of averages says San Francisco is due for a relatively healthy run, and there would be no better time for it to occur than in 2026 for a roster firmly in “win-now” mode in what has become an NFC West arms race between the Seahawks, Rams, and 49ers.
If that scenario unfolds, they will be legitimate Super Bowl contenders and strong candidates to capture that elusive Lombardi Trophy that has evaded them in the Kyle Shanahan era.
This analysis continues in the 2026 Football Preview
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