The Gators announced the deal Friday, a day after San Francisco's season ended with a first-round NCAA tournament loss Thursday night.
He will receive a six-year contract worth $3 million annually.
"We're incredibly excited about bringing in Todd, who is an innovative, relationship-oriented coach, to lead our men's basketball program,'' Florida athletic director Scott Stricklin said in a statement. "Todd brings a smart and analytics-driven approach to the game and a relational approach to leadership that puts student-athletes first.
"He has a wide range of experience, particularly for a coach his age, and brings an outstanding track record and high level of integrity to the job.''
Golden, 36, led San Francisco to the school's first NCAA tournament bid since 1998. He guided the Dons to a 24-10 record this season, which included a No. 10 seed in the NCAA tournament. San Francisco fell to No. 7 Murray State 92-87 in an overtime thriller in Indianapolis on Thursday night.
In three seasons at San Francisco, Golden compiled a 57-36 record. That included an upset of then-No. 4 Virginia in November 2020.
The qualities that attracted him to Florida officials included his ability to innovate and connect with players, fitting the mold of other young and hungry coaches who have had success there. Golden impressed Florida officials with his fluency in analytics. Golden learned under noted analytics maestro Kyle Smith, who is now the coach at Washington State.
"I'm energized by the opportunity to lead an elite program at Florida, and I'm ready to get started,'' Golden said. "Florida has a championship-level athletic department, university and men's basketball program, and I embrace the standard of excellence at Florida and the passion of Gator Nation. We couldn't be more excited about what the future holds in Gainesville.''
Golden's career before taking over at San Francisco in 2017 included assistant coach stops at San Francisco, Auburn and Columbia. The stop at Auburn gives him familiarity in the SEC, as he served both in an operations role and as an assistant coach there from 2014 to 2016.
Golden's San Francisco team this year built an identity as a rugged defensive team, ranking in the Top 25 in KenPom statistics in overall defense (adjusted for efficiency), average defensive possession length and 3-point defense. San Francisco's wins this season included Arizona State, UAB and Davidson.
In the WCC, Golden went up against top-flight coaches like Mark Few (Gonzaga), Randy Bennett (Saint Mary's), Herb Sendek (Santa Clara) and Mark Pope (BYU). That's something that will carry over to an SEC that's establishing itself as a go-to destination for top coaches.
Golden is from Phoenix, walked on at Saint Mary's to play for Bennett and worked his way to becoming a scholarship player and team captain. He played professionally for two seasons for Maccabi Haifa in Israel's top division.
Golden takes over for Mike White, who plateaued at Florida after some early success and left for Georgia last week after going 142-88 in seven seasons. White replaced Billy Donovan, who won two national titles there and was the best coach in school history.
Florida is one of the six SEC jobs to open this offseason. Georgia, Mississippi State, South Carolina, Missouri and LSU all moved on from their coaches.