The 49ers are flawed. Can Kyle Shanahan’s brain be the difference?

SANTA CLARA, Calif. — Inside the conference room, there are desks and chairs, a whiteboard and markers, and a projector.
Put San Francisco 49ers coach Kyle Shanahan in front, and, according to running back Christian McCaffrey, you’ve got football heaven.
“As a football nerd, you just learn so much every week,” McCaffrey said of the team’s weekly offensive meetings, where cool ideas fly around the room.
“It makes it a little easier with guys like Christian because he sits in probably the most boring football meetings ever,” Shanahan said. “It’s the most exciting thing known to man because he’s a true football nut.”
Shanahan’s game plan against the Seattle Seahawks defense didn’t get off the ground, all but ending his bid for his first Coach of the Year award … but that’s OK. That was the regular season. This Sunday afternoon in Philadelphia …
“It’s playoff time now,” McCaffrey said.
The 12-5 49ers still have some of the league’s best offensive players planning to run free Sunday against the Philadelphia Eagles, thanks to Shanahan’s play design. Confidence is high, and it should be, given his track record in the playoffs.
Shanahan is 8-4 in the postseason, with two wins in each of his four trips, never losing before the NFC Championship Game. The Niners are tied for third-most playoff wins since he arrived in 2017, behind only the Kansas City Chiefs (17) and Eagles (10). Three of the four losses came in close games in which the 49ers led in the fourth quarter, and the other came after they lost starting quarterback Brock Purdy to injury on their first possession (against Philadelphia).
“He’s a Hall of Fame coach,” Purdy said. “To be able to have him draw up stuff and scheme stuff for us and put guys in certain positions … we’re grateful to be playing for him.
“Any time we step out on the field with him as our play caller, we’re always going to have a chance.”
That includes on the road, as the 49ers are one of only four teams with multiple road playoff wins since 2021. They lost to Philadelphia in January 2023 after Purdy injured his elbow. Shanahan said this week the Eagles crowd is no joke.
“They’re going to be (loud),” Shanahan said. “You’ve got to give them a reason to be quiet. And if not, it’s an extremely challenging place to play. You’re not going to be able to hear, and we’ve got to expect that.”
It would be nice if Shanahan rediscovers some mojo this week.
A week after he was a step ahead of the Chicago Bears — deploying fullback Kyle Juszczyk in various motions to open lanes for McCaffrey, among other things — Shanahan ran into a brick wall against the Seahawks defense. The 49ers scored three points after putting up 127 in the previous three games.
Left tackle Trent Williams’ absence weakened the efforts — and the resolve — to run the ball. Purdy was unable to make throws off scrambles. That element, along with his ability to make the scheduled reads and throws in Shanahan’s offense, had taken the 49ers to another level the previous six weeks.
Kyle Shanahan, center right, and the 49ers won 12 games despite missing top players like George Kittle, right, to injuries for much of the season. (Lachlan Cunningham / Getty Images)
Now Shanahan and Purdy get to face an Eagles defense that has given up an NFL-best 14.5 points per game since acquiring Jaelan Phillips before Week 10. Defensive coordinator Vic Fangio makes defenses adjust to him, and then he pulls the rug out.
“Schematically, he has always been the best to me,” Shanahan said of Fangio. “As good as anyone there is. Has a very sound scheme that he doesn’t need to change up very much. It just naturally changes with how he does his coverages, how he does his fronts, the personnel groupings he does. He’s very good at getting a bead on what you’re trying to do and making you adjust.”
Shanahan said he has tried to hire Fangio three times (whenever Fangio has been in between jobs), and the two have become friends. It was born out of mutual admiration. Fangio has enjoyed his studies of the 49ers offense.
“Everything’s packaged well together,” Fangio said. “They give you a lot of good motions, and he’s a good play caller during the game. You always know that. Everything they do has a purpose and a reason.”
Fangio has had the upper hand in their head-to-head meetings. He is 3-1 against Shanahan, allowing a total of 41 points. But they haven’t faced off since 2018. Assuming Williams is back this week (he didn’t practice Wednesday), the 49ers hope to resemble the high-powered offense — featuring Purdy, McCaffrey and tight end George Kittle — that was making their punter obsolete before the loss to the Seahawks.
Shanahan is clearly not the coach he was seven years ago. Though he has done a great job keeping an injury-ravaged team together and relating with players, that’s not what makes him stand out.
It’s “his knowledge,” McCaffrey said. “His understanding of not just offensive football but defensive football as well. That allows us to open up, not just in the run game but in the pass game. He really understands gap integrity and everybody’s responsibility on defense.”
Not only that, but Shanahan taps into a defense’s emotions.
“He sees it better than anybody and plays not just to the structure of the defense but the emotions of the defense as well,” McCaffrey said. “If some guy is an aggressive guy, he knows that.”
And if Shanahan knows that, you can be sure he’s acutely aware of his own team’s weaknesses. Like his hobbled defense, even if he refuses to use it as an excuse.
Missing Fred Warner, Nick Bosa, first-round pick Mykel Williams and a slew of others because of injury, San Francisco’s defense averaged -0.06 expected points added per play in the regular season. That ranked 25th in the NFL, worst of the league’s 14 playoff teams and comfortably the worst unit of any 49ers playoff team during Shanahan’s tenure. The 2021 defense was next-worst at +0.01 EPA per play, which ranked 13th.
“We have to help out our defense,” Kittle said earlier this season. “Our offense has to play at a high level: efficient, not turn the ball over, score points, score in the red zone. Then we’ll win a lot of games. But if we’re not doing that …”
The Niners offense averaged 0.06 EPA per play (eighth-best) and 0.08 in Purdy’s nine starts, which would have ranked sixth. Since Purdy returned from his toe injury in Week 11, the offense has averaged 0.11 EPA per play despite the setback against Seattle, ranking third over that span.
Will it be enough to carry a depleted defense? Can Shanahan’s scribbles on his iPad give the Niners the edge once again in the postseason, when matchups and individual game plans become even more critical?
“I think it’s something that he was born to do,” McCaffrey said. “He’s been doing it for a long time at the highest level.
“He’s one of the best football minds ever.”
Pardon the tired cliche, but it will be a chess match on Sunday — albeit with fans shouting obscenities — and Shanahan will have his pawns and knights, like McCaffrey, ready, believing they will win.




