| Periodo | Entrenador | G (TR) | P (TR) | E (TR) | G (Pl) | P (Pl) | G | P | E | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1950-1954 | Lawrence “Buck” Shaw | 33 | 25 | 2 | 33 | 25 | 2 | ||||
| 1955 | Norman “Red” Strader | 4 | 8 | 0 | 4 | 8 | 0 | ||||
| 1956-1958 | Frankie Albert | 19 | 16 | 1 | 0 | 1 | 19 | 17 | 1 | ||
| 1959-1963 | Howard “Red” Hickey * | 27 | 27 | 1 | 27 | 27 | 1 | ||||
| 1963-1967 | Jack Christiansen | 26 | 38 | 3 | 26 | 38 | 3 | ||||
| 1968-1975 | Dick Nolan | 54 | 53 | 5 | 2 | 3 | 56 | 56 | 5 | ||
| 1976 | Monte Clark | 8 | 6 | 0 | 8 | 6 | 0 | ||||
| 1977 | Ken Meyer | 5 | 9 | 0 | 5 | 9 | 0 | ||||
| 1978 | Pete McCulley ** | 1 | 8 | 0 | 1 | 8 | 0 | ||||
| (Int.) 1978 | Fred O´Connor | 1 | 6 | 0 | 1 | 6 | 0 | ||||
| 1979-1988 | Bill Walsh | 92 | 59 | 1 | 10 | 4 | 102 | 63 | 1 | ||
| 1989-1996 | George Seifert | 98 | 30 | 0 | 10 | 5 | 108 | 35 | 0 | ||
| 1997-2002 | Steve Mariucci | 57 | 39 | 0 | 3 | 4 | 60 | 43 | 0 | ||
| 2003-2004 | Dennis Erickson | 9 | 23 | 0 | 9 | 23 | 0 | ||||
| 2005-2008 | Mike Nolan *** | 18 | 37 | 0 | 18 | 37 | 0 | ||||
| 2008-2010 | Mike Singletary # | 18 | 22 | 0 | 18 | 22 | 0 | ||||
| 2010 | Jim Tomsula | 1 | 0 | 0 | 1 | 0 | 0 | ||||
| 2011-2014 | Jim Harbaugh | 44 | 19 | 1 | 5 | 3 | 49 | 22 | 1 | ||
| 2015 | Jim Tomsula | 5 | 11 | 0 | 5 | 11 | 0 | ||||
| 2016 | Chip Kelly | 2 | 14 | 0 | 2 | 14 | 0 | ||||
| 2017- | Kyle Shanahan | 76 | 65 | 0 | 8 | 4 | 84 | 69 | 0 | ||
| TOTAL | 574 | 496 | 14 | 36 | 23 | 610 | 519 | 14 |
** Despedido después de 9 juegos en 1978
*** Despedido después de 7 juegos en 2008
# Despedido después de 15 juegos en 2010
(Int.): Head Coach Interino