| NAME | TD | SEASON | TM | GP | CMP | ATT | PCT | YDS | AVG | YDS/G | INT | RTG | TD% | INT% | SCK | SCKY | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 |  | S. Young | 36 | 1998 |  SF | 15 | 322 | 517 | 62.3 | 4,170 | 8.1 | 278.0 | 12 | 101.1 | 7.0 | 2.3 | 48 | 234 |
| 2 | | S. Young | 35 | 1994 | SF | 16 | 324 | 461 | 70.3 | 3,969 | 8.6 | 248.1 | 10 | 112.8 | 7.6 | 2.2 | 31 | 163 |
| 3 |  | J. Garcia | 32 | 2001 | SF | 16 | 316 | 504 | 62.7 | 3,538 | 7.0 | 221.1 | 12 | 94.8 | 6.3 | 2.4 | 26 | 114 |
| 4 |  | B. Purdy | 31 | 2023 | SF | 16 | 308 | 444 | 69.4 | 4,280 | 9.6 | 267.5 | 11 | 113.0 | 7.0 | 2.5 | 28 | 153 |
| 5 | | J. Garcia | 31 | 2000 | SF | 16 | 355 | 561 | 63.3 | 4,278 | 7.6 | 267.4 | 10 | 97.6 | 5.5 | 1.8 | 24 | 155 |
| 6 |  | J. Montana | 31 | 1987 | SF | 13 | 266 | 398 | 66.8 | 3,054 | 7.7 | 234.9 | 13 | 102.1 | 7.8 | 3.3 | 22 | 158 |
| 7 | | J. Brodie | 30 | 1965 | SF | 13 | 242 | 391 | 61.9 | 3,112 | 8.0 | 239.4 | 16 | 95.3 | 7.7 | 4.1 | ||
| 8 | | S. Young | 29 | 1993 | SF | 16 | 314 | 462 | 68.0 | 4,023 | 8.7 | 251.4 | 16 | 101.5 | 6.3 | 3.5 | 31 | 160 |
| 9 | | J. Montana | 28 | 1984 | SF | 16 | 279 | 432 | 64.6 | 3,630 | 8.4 | 226.9 | 10 | 102.9 | 6.5 | 2.3 | 22 | 138 |
| 10 |  | J. Garoppolo | 27 | 2019 | SF | 16 | 329 | 476 | 69.1 | 3,978 | 8.4 | 248.6 | 13 | 102.0 | 5.7 | 2.7 | 36 | 237 |
| 11 | | J. Montana | 27 | 1985 | SF | 15 | 303 | 494 | 61.3 | 3,653 | 7.4 | 243.5 | 13 | 91.3 | 5.5 | 2.6 | 35 | 246 |
| 12 | | J. Montana | 26 | 1990 | SF | 15 | 321 | 520 | 61.7 | 3,944 | 7.6 | 262.9 | 16 | 89.0 | 5.0 | 3.1 | 29 | 153 |
| 13 | | J. Montana | 26 | 1989 | SF | 13 | 271 | 386 | 70.2 | 3,521 | 9.1 | 270.8 | 8 | 112.4 | 6.7 | 2.1 | 33 | 198 |
| 14 | | J. Montana | 26 | 1983 | SF | 16 | 332 | 515 | 64.5 | 3,910 | 7.6 | 244.4 | 12 | 94.6 | 5.0 | 2.3 | 33 | 224 |
| 15 | | S. Young | 25 | 1992 | SF | 16 | 268 | 402 | 66.7 | 3,465 | 8.6 | 216.6 | 7 | 107.0 | 6.2 | 1.7 | 29 | 152 |
| 16 | | J. Brodie | 24 | 1970 | SF | 14 | 223 | 378 | 59.0 | 2,941 | 7.8 | 210.1 | 10 | 93.8 | 6.3 | 2.6 | 8 | 67 |
| 17 | | J. Brodie | 22 | 1968 | SF | 14 | 234 | 404 | 57.9 | 3,020 | 7.5 | 215.7 | 21 | 78.0 | 5.4 | 5.2 | ||
| 18 |  | C. Kaepernick | 21 | 2013 | SF | 16 | 243 | 416 | 58.4 | 3,197 | 7.7 | 199.8 | 8 | 91.6 | 5.0 | 1.9 | 39 | 231 |
| 19 | | J. Garcia | 21 | 2002 | SF | 16 | 328 | 528 | 62.1 | 3,344 | 6.3 | 209.0 | 10 | 85.6 | 4.0 | 1.9 | 17 | 93 |
| 20 | | B. Purdy | 20 | 2024 | SF | 15 | 300 | 455 | 65.9 | 3,864 | 8.5 | 257.6 | 12 | 96.1 | 4.4 | 2.6 | 31 | 156 |
| 21 | | J. Garoppolo | 20 | 2021 | SF | 15 | 301 | 441 | 68.3 | 3,810 | 8.6 | 254.0 | 12 | 98.7 | 4.5 | 2.7 | 29 | 201 |
| 22 | | S. Young | 20 | 1995 | SF | 11 | 299 | 447 | 66.9 | 3,200 | 7.2 | 290.9 | 11 | 92.3 | 4.5 | 2.5 | 25 | 115 |
| 23 | | Y.A. Tittle | 20 | 1953 | SF | 11 | 149 | 259 | 57.5 | 2,121 | 8.2 | 192.8 | 16 | 84.1 | 7.7 | 6.2 | ||
| 24 | | C. Kaepernick | 19 | 2014 | SF | 16 | 289 | 478 | 60.5 | 3,369 | 7.0 | 210.6 | 10 | 86.4 | 4.0 | 2.1 | 52 | 344 |
| 25 | | S. Young | 19 | 1997 | SF | 15 | 241 | 356 | 67.7 | 3,029 | 8.5 | 201.9 | 6 | 104.7 | 5.3 | 1.7 | 35 | 220 |
StatMuse has season-level data for passing touchdowns going back to the 1921 season.
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