49ers struck gold with John Lynch, Kyle Shanahan after years of dysfunction

Kyle Shanahan and John Lynch have proven to be a good pairing since they came to the 49ers together with matching six-year contracts in 2017.

Now, both have contract extensions that will keep them together beyond their original contracts.

Lynch strongly hinted Tuesday during an appearance on KNBR that he would soon be signing a new contract. A day later, a league source confirms reports that Lynch’s new deal is agreed upon.

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It might not have been so much how Shanahan and Lynch worked together last season en route to a Super Bowl appearance that convinced 49ers CEO Jed York to sign them to extensions. All the evidence he needed showed up during their first two seasons together when the 49ers won just 10 games.

Lynch and Shanahan worked well together and never wavered even during difficult times.

With a depleted roster inherited from Trent Baalke’s reign as general manager, the 49ers had to find the right general manager for Shanahan, who left his position as Atlanta Falcons offensive coordinator to take over the 49ers.

Shanahan is fiery and does not hold back what he’s thinking. When he sat down with York during the interview process, Shanahan told York he thought the team’s roster was horrible. It was going to be a difficult transition, and York needed to show his new coach and GM that he was committed to a rebuilding process with six-year contracts.

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There would be difficult days ahead, and Shanahan needed a general manager who could help him manage his emotions and keep him sane through loss after loss after loss. He found that person in Lynch. And those two have made York's job a lot easier, too.

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Lynch, coming straight from the FOX broadcast booth, was an outside-the-box selection. But in his third season as GM, Lynch was named NFL Executive of the Year by the Pro Football Writers of America. That hire clearly was the correct move.

And Shanahan became the first 49ers head coach to sign an extension since Steve Mariucci in 1999. His new deal, which was agreed upon shortly after the team’s Super Bowl loss, runs through the 2025 season.

Lynch has a new deal that runs through 2024.

It made sense that there was a greater priority to get Shanahan signed to a new deal first. His original six-year, $30 million contract ranked near the bottom of the NFL and had been passed by Cincinnati Bengals coach Zac Taylor, who was hired in 2019.

Lynch’s original deal was believed to pay him $20 million over six seasons – a contract that kept him among the top-paid general managers in the league. Lynch was well-paid as a TV analyst, so the 49ers had to provide a competitive salary to entice him to join their front office.

The only surprise with Lynch agreeing to an extension is that his contract no longer matches up with Shanahan in years. Lynch’s new deal expires one year before Shanahan’s.

Shanahan, 40, the son of two-time Super Bowl-winning head coach Mike Shanahan, was born to coach. He has a long career ahead of him. He has never wanted to do anything else.

But Lynch, 48, made an interesting comment during an appearance on KNBR on Tuesday when he revealed his contract extension was “on the horizon.”

“I don’t know if I’m going to be a lifer at this thing, but I love what we’re doing,” Lynch said.

[RELATED: Report: Kittle, 49ers still not close on any contract talks]

Perhaps, Lynch already has decided he does not want to spend most of the rest of his life in the daily grind of an NFL front-office job. The 49ers have others in the organization -- namely, Martin Mayhew and Adam Peters -- who are more than capable of stepping into a general manager position.

This deal signals Lynch is not going anywhere any time soon.

It also provides a reminder after all the organizational dysfunction of the past two decades, the 49ers should cherish this union of Shanahan and Lynch for as long as they have them together.

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