27 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Atchison | 1 | 10,800 | 10,878 | -0.12% | 1,347 | 8 | City |
| Atchison | 2 | 10,800 | 10,865 | -0.12% | 1,347 | 8 | City |
| Shannon | 3 | 1,142 | 1,149 | 0.53% | 22 | 52 | Township |
| Shannon | 4 | 1,142 | 1,148 | 0.53% | 22 | 52 | Township |
| Mount Pleasant | 5 | 875 | 862 | 1.04% | 18 | 48 | Township |
| Mount Pleasant | 6 | 875 | 861 | 1.04% | 18 | 48 | Township |
| Lancaster | 7 | 751 | 749 | 0.67% | 12 | 60 | Township |
| Lancaster | 8 | 751 | 748 | 0.67% | 12 | 60 | Township |
| Center | 9 | 627 | 622 | 0.8% | 12 | 54 | Township |
| Center | 10 | 627 | 621 | 0.8% | 12 | 54 | Township |
| Grasshopper | 11 | 507 | 508 | 0.6% | 8 | 66 | Township |
| Grasshopper | 12 | 507 | 508 | 0.6% | 8 | 66 | Township |
| Effingham | 13 | 485 | 493 | -0.41% | 784 | 1 | City |
| Effingham | 14 | 485 | 492 | -0.41% | 784 | 1 | City |
| Kapioma | 15 | 254 | 254 | 0.79% | 5 | 47 | Township |
| Kapioma | 16 | 254 | 254 | 0.79% | 5 | 47 | Township |
| Lancaster | 17 | 244 | 244 | 0% | 1,226 | 0 | City |
| Lancaster | 18 | 244 | 244 | 0% | 1,226 | 0 | City |
| Kickapoo Site 5 | 19 | 170 | 75 | 6.92% | 227 | 1 | CDP |
| Muscotah | 20 | 155 | 157 | -0.64% | 465 | 0 | City |
| Muscotah | 21 | 155 | 157 | -0.64% | 465 | 0 | City |
| Kickapoo Tribal Center | 22 | 114 | 155 | -4.2% | 59 | 2 | CDP |
| Kickapoo Site 1 | 23 | 94 | 92 | 0% | 188 | 1 | CDP |
| Kickapoo Site 7 | 24 | 78 | 61 | 8.33% | 154 | 1 | CDP |
| Huron | 25 | 74 | 74 | 0% | 1,028 | 0 | City |
| Huron | 26 | 74 | 74 | 0% | 1,028 | 0 | City |
| Kickapoo Site 2 | 27 | 27 | 57 | 3.85% | 32 | 1 | CDP |
Atchison is the largest city in Atchison County, with a population of 10,800.
Kickapoo Site 2 is the smallest city in Atchison County, with a population of 27.
There are 27 cities in Atchison County, Kansas.