Klay Kubiak is in his sixth season with the 49ers and second as the team's offensive coordinator. He spent the 2024 season as San Francisco's offensive passing game specialist and served two seasons (2022-23) as the 49ers assistant quarterbacks coach after spending the 2021 season as a defensive quality control coach with the team. Kubiak joined the 49ers after spending the previous three years (2018-20) as the head coach at Strake Jesuit College Preparatory (Houston, TX). He also served as the school's offensive coordinator from 2013-15 and for the 2017 season.

Kubiak helped guide the 2025 49ers offense to top-10 rankings in multiple categories. The unit finished the season near the top of the NFL in third down conversion percentage (49.8% – first), average first downs per game (22.3 – third), passing yards per game (244.5 – fifth), red zone efficiency (65.2% – tied-for-fifth), total yards (5,974 – seventh), yards per game (351.4 – tied-for-seventh) and points per game (25.7 – 10th). The unit also registered the third-most first downs in the NFL (379), 237 of which were passing first downs, which led the NFL and marked the most in a single season in franchise history. San Francisco's offense featured three selections to the Associated Press All-Pro team in FB Kyle Juszczyk (First-Team), RB Christian McCaffrey (First-Team) and T Trent Williams (Second-Team). McCaffrey also earned AP NFL Comeback Player of the Year honors after finishing the season with 311 carries for 1,202 yards and 10 touchdowns on the ground to go along with 102 receptions for 924 yards and seven touchdowns through the air. McCaffrey led the team in rushing yards, receiving yards and rushing touchdowns, while his 413 total touches were the most in the NFL.

Klay Kubiak is in his sixth season with the 49ers and second as the team's offensive coordinator. He spent the 2024 season as San Francisco's offensive passing game specialist and served two seasons (2022-23) as the 49ers assistant quarterbacks coach after spending the 2021 season as a defensive quality control coach with the team. Kubiak joined the 49ers after spending the previous three years (2018-20) as the head coach at Strake Jesuit College Preparatory (Houston, TX). He also served as the school's offensive coordinator from 2013-15 and for the 2017 season.

Kubiak helped guide the 2025 49ers offense to top-10 rankings in multiple categories. The unit finished the season near the top of the NFL in third down conversion percentage (49.8% – first), average first downs per game (22.3 – third), passing yards per game (244.5 – fifth), red zone efficiency (65.2% – tied-for-fifth), total yards (5,974 – seventh), yards per game (351.4 – tied-for-seventh) and points per game (25.7 – 10th). The unit also registered the third-most first downs in the NFL (379), 237 of which were passing first downs, which led the NFL and marked the most in a single season in franchise history. San Francisco's offense featured three selections to the Associated Press All-Pro team in FB Kyle Juszczyk (First-Team), RB Christian McCaffrey (First-Team) and T Trent Williams (Second-Team). McCaffrey also earned AP NFL Comeback Player of the Year honors after finishing the season with 311 carries for 1,202 yards and 10 touchdowns on the ground to go along with 102 receptions for 924 yards and seven touchdowns through the air. McCaffrey led the team in rushing yards, receiving yards and rushing touchdowns, while his 413 total touches were the most in the NFL.

In addition to McCaffrey, the 49ers offensive unit also featured WR Jauan Jennings, who added 55 receptions for 643 yards and a career-high nine touchdowns, and TE George Kittle, who finished the season with 57 receptions for 628 yards and seven touchdowns. Kubiak also worked closely with QB Brock Purdy and QB Mac Jones. In nine starts on the season, Purdy completed 197 of his 284 passing attempts (69.4%) for 2,167 yards and 20 touchdowns with a passer rating of 100.5. Jones started eight games in relief and led the team to five wins by completing 201 of his 289 passing attempts (69.6%) for 2,151 yards and 13 touchdowns with a career high passer rating of 97.4. Jones' 69.6% completion percentage also marked a career high.

In 2024, Kubiak helped direct a 49ers offense that finished tied for second in yards per play (6.2) and fourth in yards per game (376.3), passing yards per game (249.1) and total yards (6,397). With his help, WR Jauan Jennings registered career highs in receptions (77), receiving yards (975) and receiving touchdowns (six). Kubiak also helped TE George Kittle earn Associated Press Second-Team All-Pro honors and the sixth Pro Bowl selection of his career after he led the team in receptions (78), receiving yards (1,106) and receiving touchdowns (eight). Kittle's 1,106 receiving yards marked his second-consecutive and fourth overall season with 1,000-or-more receiving yards, making him one of five tight ends in NFL history to register four such seasons. Kubiak also worked closely with QB Brock Purdy, helping him set the NFL records for the most games with a passer rating of 140.0-or-higher (six), 130.0-or-higher (10) and 120.0-or-higher (13) by a quarterback in their first three seasons.

The 2023 San Francisco 49ers saw Purdy lead the NFL in passer rating (113.0) and yards per attempt (9.6), while setting the franchise record for passing yards (4,280) and throwing 31 touchdowns. In his first year as a starter, Purdy became the first 49ers QB to throw 30-or-more touchdowns in a single season in 22 years and the first 49ers QB selected to a Pro Bowl since QB Jeff Garcia in 2002, leading the team to a spot in Super Bowl LVIII.