The Pros and Cons of the 49ers Potentially Extending Kyle Shanahan

The positives, negatives, and implications.

Sep 28, 2025; Santa Clara, California, USA; San Francisco 49ers head coach Kyle Shanahan during the second quarter against the Jacksonville Jaguars at Levi's Stadium. Mandatory Credit: Darren Yamashita-Imagn Images | Darren Yamashita-Imagn Images

The Niners are off to a 5-2 start despite seemingly half the team going down with injury, and Kyle Shanahan is a Coach of the Year candidate. This year, and the nine that preceded it, have led the dean of 49ers beat writers to say this:

"Shanahan almost assuredly will become the longest-tenured coach in franchise history. And while nothing lasts forever, it is difficult to envision this union having an expiration date."–Matt Maiocco, NBC Sports Bay Area.

Maiocco hasn’t reported that an extension is imminent; he’s just applying logic here, but it’s hard to argue with him. Shanahan is under contract through the 2027 season. In the past, extension talks with Shanahan have been kept quiet and announced long after a deal has been reached.

If Shanahan is extended, nearly all Niner fans will form a conga line, a few will gripe, and I, being the resident curmudgeon, will say, ok, no rings for you. By the way, that has nothing to do with Shanahan as coach or offensive coordinator. Let’s break it down.

Positives

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Shanahan is one of the top offensive minds in the game and is having what may well be his most creative season in dealing with the perpetual injuries. He is a key element of the team’s identity with his proven offensive system, and keeps his team motivated and prepared every week when the consensus is nope, they’re too injured to win this one. Shanahan and defensive coordinator Robert Saleh keep finding a way.

The NFL coaching model that typically succeeds is to keep the offensive coordinator locked in as head coach. Look through the teams with the best records right now and most are led by offensive minds.

A frequent point of fans is essentially a lack of faith in the alternatives, and in the Yorks to pick one that will succeed. Invariably, when the discussion turns to letting go of Shanahan, the Faithful cast the Expecto Tomsula spell. The past failures are a bitter memory, and they don’t want to return to being the punchline of jokes from opposing fans.

There is a generational divide in the fanbase. The younger fans who haven’t seen rings live value consistent contention; being in the mix is enough for them. The older fans dating back to Bill Walsh (raises hand) are rings or bust. There is no reconciliation between the two.

Few coaches have Shanahan’s level of success  — two Super Bowl appearances, frequently in contention, typically in the mix year to year. The Yorks business model relies on frequent contention to keep Levi’s full, and Shanahan continues to lay golden eggs.

Negatives

Darren Yamashita-Imagn Images

Start with the perpetual injuries. 49er content creator Johnny Dels looked at the probability numbers recently. The Niners being one of the ten most injured teams in the league for eight of the past nine seasons can’t be written off as “that’s just football.”

Dels’ analysis notes that the chances the Niner injury record is just bad luck comes in at 0.059%. Or flipped around, there is a 99.941% chance that the Niner injury problems have a basis in process. That’s not to say there aren’t fluke injuries, that happens, but injuries at this volume have root causes.

Shanahan’s defenders will accurately point out that the Niner injury problems predated his arrival. My counter to that argument is regardless of when it began, what have Shanahan and the organization done to fix it? Very little.

Strength and conditioning people are fired, but replacements are promoted from within. Where is the long-overdue best practices analysis to determine which teams are staying healthy and why? Why haven’t the staff from those teams been poached?

The Niners are on pace to have the most injured team in the league for the third time in four years. This has been swept under the rug for years. Do I expect the Yorks to mandate that the strength and conditioning staff be fired en masse? No. Do I expect Shanahan or John Lynch to do that? No. So the problem continues unaddressed.

Darren Yamashita-Imagn Images

Next, the black box of the San Francisco 49ers, personnel decisions. Lynch added some clarity when he said, “Kyle has the 53, I have the 90.” That lines up with the expected hierarchy, that Shanahan has final authority on personnel. When he uses that is unknown. Which picks are from Shanahan, Lynch, the front office and the scouts? It is purposefully vague as the participants talk about collaboration, but that shrouds accountability.

We know from media reports that trading up for Joe Williams was Shanahan’s call. Lynch told him the scouts had Williams as undrafted. Shanahan was sold though, and they picked him. Never played a down for the team.

We can guess that Shanahan picks the weapons, but that's a guess, and may be true most of the time but not all. All we can say is this. The Trey Lance trade was a disaster and the Niners had arguably the worst draft in the league in both 2022 and 2023.  

We know this team has drafted ten offensive linemen and 17 wide receivers in the last nine years; that certainly sounds like Shanahan, and he has said he values those who touch the ball.

All those weapon busts living on the Island of Misfit Toys sounds like Shanahan to me, can’t prove it though. Regardless, it happened and has done the team no favors. Ten linemen and 17 receivers is not how you build a team. Vetoing the Brandon Aiyuk trade to Pittsburgh that would have landed the 20th pick in the best offensive lineman draft in over a decade is not how you build a team either.

Despite all those miscues, the Niners drafted well in the past two years, and 2026 will be the acid test. Will they finally draft a left tackle and a center early or take a receiver in the first?  Will they trade up for the top tight end or running back?

In Part 2, I’ll have a projected Shanahan mock. Also, a discussion of the roster implications going forward if Maiocco is correct and Shanahan is here for the long haul.