35 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Farmington | 1 | 46,203 | 46,608 | -0.13% | 1,341 | 34 | City |
| Farmington | 2 | 46,203 | 46,497 | -0.13% | 1,341 | 34 | City |
| Shiprock | 3 | 8,270 | 8,588 | -0.02% | 612 | 14 | CDP |
| Bloomfield | 4 | 7,351 | 7,431 | -0.16% | 396 | 19 | City |
| Bloomfield | 5 | 7,351 | 7,411 | -0.16% | 396 | 19 | City |
| Aztec | 6 | 6,111 | 6,216 | -0.29% | 358 | 17 | City |
| Aztec | 7 | 6,111 | 6,200 | -0.29% | 358 | 17 | City |
| Crouch Mesa | 8 | 6,042 | 4,626 | 7.13% | 292 | 21 | CDP |
| Lee Acres | 9 | 4,608 | 5,318 | -1.77% | 446 | 10 | CDP |
| Center Point | 10 | 3,220 | 2,726 | 7.15% | 350 | 9 | CDP |
| La Plata | 11 | 2,426 | 2,078 | 5.25% | 109 | 22 | CDP |
| Flora Vista | 12 | 2,385 | 2,187 | 0.55% | 482 | 5 | CDP |
| Angustura | 13 | 2,355 | 2,050 | 7.14% | 494 | 5 | CDP |
| West Hammond | 14 | 2,315 | 2,738 | -1.36% | 254 | 9 | CDP |
| South River | 15 | 1,980 | 2,248 | 7.14% | 232 | 9 | CDP |
| Upper Fruitland | 16 | 1,501 | 1,601 | -0.73% | 196 | 8 | CDP |
| Waterflow | 17 | 1,239 | 1,552 | -2.29% | 153 | 8 | CDP |
| Spencerville | 18 | 1,153 | 1,592 | -0.6% | 219 | 5 | CDP |
| Cedar Hill | 19 | 952 | 901 | 0.74% | 101 | 9 | CDP |
| North Light Plant | 20 | 791 | 860 | 3.26% | 366 | 2 | CDP |
| Napi Headquarters | 21 | 603 | 717 | -1.47% | 135 | 4 | CDP |
| Kirtland | 22 | 572 | 584 | -0.35% | 332 | 2 | Town |
| Kirtland | 23 | 572 | 582 | -0.35% | 332 | 2 | Town |
| Totah Vista | 24 | 570 | 366 | 7.14% | 997 | 1 | CDP |
| Newcomb | 25 | 459 | 535 | 1.77% | 47 | 10 | CDP |
| Blanco | 26 | 437 | 465 | 0.69% | 71 | 6 | CDP |
| Fruitland | 27 | 430 | 610 | 7.23% | 220 | 2 | CDP |
| Sheep Springs | 28 | 391 | 397 | 2.36% | 76 | 5 | CDP |
| Nenahnezad | 29 | 376 | 470 | -5.05% | 107 | 4 | CDP |
| Navajo Dam | 30 | 342 | 378 | 1.18% | 28 | 12 | CDP |
| Nageezi | 31 | 327 | 266 | 0.93% | 23 | 14 | CDP |
| Ojo Amarillo | 32 | 325 | 529 | -8.19% | 165 | 2 | CDP |
| Sanostee | 33 | 252 | 428 | -3.08% | 56 | 5 | CDP |
| Beclabito | 34 | 218 | 275 | -3.11% | 29 | 8 | CDP |
| Lake Valley | 35 | 123 | 96 | 7.89% | 15 | 8 | CDP |
Farmington is the largest city in San Juan County, with a population of 46,203.
Lake Valley is the smallest city in San Juan County, with a population of 123.
There are 35 cities in San Juan County, New Mexico.