A lot has been written about the outstanding performance of San Francisco’s coaching staff this year. Head coach Kyle Shanahan deserves all the praise for the work he’s done with the offense and the overall team chemistry. Defensive coordinator Robert Saleh, of course, is possibly the most valuable coordinator in the game right now, having coached up a young, injury-riddled defense and brought fire to a team that looked mostly disinterested in 2024.

Lastly, rounding out all 3 phases, Brant Boyer has put together one of the most efficient and reliable special teams units in the NFL, a complete reversal from last season and a trend-breaker from most of Shanahan’s tenure as head coach.

The 49ers were supposed to be in a rebuilding year. While they are in the process of getting younger, cheaper, and learning who their new stalwarts will be heading into the back half of this decade, they’re right in the thick of the NFC playoff race and contending to play home games in January.

Watching the 49ers handle their business against the Browns on Sunday, one element of the game that hasn’t garnered much attention this year is how San Francisco has dramatically improved in avoiding penalties. For all the success they’ve had over the last six seasons, penalties have bogged them down at times, and for all the creativity and “genius” that comes from this team’s coaching, discipline in avoiding flags has been a weak point.

Not so in 2025.

Per NFLPenalties.com, San Francisco currently ranks second in the league in penalties per game and penalties per play (Rams lead in both categories) through the first 13 weeks. Should they maintain this trend, it would be the first time since the 2019 season’s Super Bowl run that they would finish in the top 10 in either category.

Setting 2019 aside, the 49ers have been in the bottom half of the league in penalties per play every year and never finished anywhere near the top 5.

2019
2020
2021
2022
2023
2024
2025

SF Per Game (Rank)
10
16
17
18
18
21
2

SF Per Play (Rank)
11
17
24
21
21
22
2

1st Place Per Game
IND
NE
GB
ATL
LV
AZ
LAR

1st Place Per Play
IND
NE
GB
ATL
LAC
IND
LAR

Last Place PG
TB
AZ
Dal
AZ
NYJ
NYJ
JAX

Last Place PP
JAX
AZ
DAL
AZ
NYJ
NYJ
JAX

Avg PG
6.69
5.56
5.86
5.55
5.67
6.4
6.65

Avg PP
3.77
3.53
3.8
3.62
3.67
4.19
4.41

Limiting penalties, particularly on defense, has been critical to the team’s ability to get its defense off the field and win in close games. Clearly, the coaching staff is doing something right in practice to take an exceedingly inexperienced group and perform this well penalty-wise. More credit to Shanahan, and especially to Saleh, who, interestingly, had his New York Jets at the bottom of the league in penalty stats over the last 2 seasons as head coach (2024 being a partial year, as he was fired early in the season).

The 49ers still have an uphill battle to reach another Super Bowl with the defensive talent gap they face against the top teams in the NFC. Still, with major improvements to special teams play and avoiding flags, they’re giving themselves every opportunity to contend.