The head coach and GM will be back with the team in 2025.

The San Francisco 49ers endured a disappointing injury-marred season in 2024. Coming off a Super Bowl appearance the previous year, in which the 49ers lost by three points in overtime to the Kansas City Chiefs, San Francisco went just 6-11 in 2024. The team missed the playoffs for the first time since a 6-10 finish in 2020.

Despite the lost season, the 49ers are forging ahead with the leadership that’s proven so successful over the last eight seasons. San Francisco’s CEO Jed York is sticking with head coach Kyle Shanahan and general manager John Lynch. “There’s no one that I respect more and trust more than John Lynch and Kyle Shanahan to get us back on track,” York said per ProFootballTalk.

This isn’t the first time the organization has expressed confidence in Shanahan and Lynch despite the brutal 2024 season. York told reporters that the duo’s jobs are secure back in Week 17 when the 49ers lost to the Detroit Lions on Monday Night Football. “They’re not going anywhere,” York said at the time. Now he’s doubling down on keeping the head coach/GM tandem in place.

The 49ers are hanging onto Kyle Shanahan and John Lynch

Shanahan and Lynch were both hired after the team bottomed out in 2016, finishing with a 2-14 record under Chip Kelly in his sole season as the 49ers’ head coach. Since taking over the team, the pair have gone 70-62 in eight seasons. They’ve led the 49ers to two Super Bowl appearances and four NFC Championship Games.

Of course, Shanahan and Lynch haven’t been able to win a title in San Francisco as the team lost Super Bowl LIV and LVIII to the Patrick Mahomes-led Chiefs. But their sustained success made the decision to retain them easy for York.

The 2024 season was an unmitigated disaster as the 49ers suffered numerous injuries to key players. Running back Christian McCaffrery was coming off his Offensive Player of the Year campaign in 2023 but was only able to play in four games this season, finishing with 348 total yards and failing to record a touchdown.

Top wideout Brandon Aiyuk suffered a season-ending injury that limited him to seven games and defensive leader Dre Greenlaw only appeared in two contests as he made his way back from an Achilles tear in the Super Bowl. That’s a small sample of the role injury played in the 49ers’ 2024 season.

While there was some talk of Shanahan being traded to the Chicago Bears, San Francisco will hang onto one of the league’s best coaches. Now the team must make some difficult decisions this offseason, including a contract extension for Brock Purdy. But the 49ers’ leadership will remain in place as the team attempts to turn things around in 2025.