Rathman, a former 49ers fullback for eight seasons and two Super Bowl titles, was San Francisco's running backs coach from 1997-2002 under coach Steve Mariucci. Rathman followed Mariucci to Detroit in 2003 before spending the last two seasons in the same job with the Oakland Raiders.
Although San Francisco coach Mike Singletary hasn't even begun interviews to replace offensive coordinator Mike Martz, he moved quickly to hire Rathman after an interview Tuesday.
Rathman was thought to be a candidate to go to Seattle with former Oakland Raiders offensive coordinator Greg Knapp, who has agreed to take the same job with new Seahawks coach Jim Mora. Knapp, Mora and Rathman all worked on Mariucci's staffs in San Francisco.