18 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Fort Atkinson | 1 | 12,326 | 12,584 | -0.41% | 2,108 | 6 | City |
| Fort Atkinson | 2 | 12,326 | 12,579 | -0.41% | 2,108 | 6 | City |
| Jefferson | 3 | 7,761 | 7,789 | -0.06% | 1,331 | 6 | City |
| Jefferson | 4 | 7,761 | 7,784 | -0.06% | 1,331 | 6 | City |
| Lake Mills | 5 | 6,705 | 6,219 | 1.33% | 1,605 | 4 | City |
| Lake Mills | 6 | 6,705 | 6,265 | 1.33% | 1,605 | 4 | City |
| Waterloo | 7 | 3,639 | 3,496 | 0.78% | 959 | 4 | City |
| Waterloo | 8 | 3,639 | 3,496 | 0.78% | 959 | 4 | City |
| Johnson Creek | 9 | 3,412 | 3,327 | 0.41% | 1,127 | 3 | Village |
| Johnson Creek | 10 | 3,412 | 3,341 | 0.41% | 1,127 | 3 | Village |
| Ixonia | 11 | 2,174 | 1,856 | 1.73% | 598 | 4 | CDP |
| Palmyra | 12 | 1,717 | 1,729 | -0.12% | 749 | 2 | Village |
| Palmyra | 13 | 1,717 | 1,727 | -0.12% | 749 | 2 | Village |
| Sullivan | 14 | 653 | 653 | 0% | 576 | 1 | Village |
| Sullivan | 15 | 653 | 652 | 0% | 576 | 1 | Village |
| Rome | 16 | 555 | 647 | -1.6% | 150 | 4 | CDP |
| Hebron | 17 | 366 | 317 | 2.52% | 148 | 2 | CDP |
| Helenville | 18 | 159 | 245 | -3.64% | 287 | 1 | CDP |
Fort Atkinson is the largest city in Jefferson County, with a population of 12,326.
Helenville is the smallest city in Jefferson County, with a population of 159.
There are 18 cities in Jefferson County, Wisconsin.