16 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Boonville | 1 | 7,932 | 8,042 | 0.88% | 958 | 8 | City |
| Boonville | 2 | 7,932 | 7,586 | 0.88% | 958 | 8 | City |
| Pilot Grove | 3 | 696 | 664 | 0.87% | 1,653 | 0 | City |
| Pilot Grove | 4 | 696 | 664 | 0.87% | 1,653 | 0 | City |
| Otterville | 5 | 451 | 441 | 0.45% | 922 | 0 | City |
| Otterville | 6 | 451 | 441 | 0.45% | 922 | 0 | City |
| Windsor Place | 7 | 363 | 353 | 0.55% | 405 | 1 | Village |
| Windsor Place | 8 | 363 | 353 | 0.55% | 405 | 1 | Village |
| Bunceton | 9 | 339 | 333 | 0.3% | 359 | 1 | City |
| Bunceton | 10 | 339 | 333 | 0.3% | 359 | 1 | City |
| Prairie Home | 11 | 267 | 262 | 0.38% | 688 | 0 | City |
| Prairie Home | 12 | 267 | 262 | 0.38% | 688 | 0 | City |
| Blackwater | 13 | 179 | 174 | 0.56% | 546 | 0 | City |
| Blackwater | 14 | 179 | 174 | 0.56% | 546 | 0 | City |
| Wooldridge | 15 | 31 | 30 | 0% | 517 | 0 | Village |
| Wooldridge | 16 | 31 | 30 | 0% | 517 | 0 | Village |
Boonville is the largest city in Cooper County, with a population of 7,932.
Wooldridge is the smallest city in Cooper County, with a population of 31.
There are 16 cities in Cooper County, Missouri.