13 cities
| City | Rank | 2025 Pop. ↓ | 2020 Pop. | Annual Change | Density | Area (mi²) | Type |
|---|---|---|---|---|---|---|---|
| Fort Madison | 1 | 9,900 | 10,313 | -0.83% | 1,026 | 10 | City |
| Keokuk | 2 | 9,354 | 9,893 | -1.14% | 1,028 | 9 | City |
| West Point | 3 | 898 | 923 | -0.55% | 1,412 | 1 | City |
| Donnellson | 4 | 852 | 887 | -0.81% | 669 | 1 | City |
| Montrose | 5 | 731 | 744 | -0.41% | 605 | 1 | City |
| Denmark | 6 | 704 | 504 | 2.62% | 424 | 2 | CDP |
| Sandusky | 7 | 455 | 312 | 7.06% | 319 | 1 | CDP |
| Mooar | 8 | 335 | 388 | 7.03% | 127 | 3 | CDP |
| Wever | 9 | 223 | 112 | 7.21% | 151 | 1 | CDP |
| Franklin | 10 | 134 | 129 | 0.75% | 859 | 0 | City |
| Houghton | 11 | 128 | 133 | -0.78% | 432 | 0 | City |
| St. Paul | 12 | 104 | 108 | -0.95% | 274 | 0 | City |
| Argyle | 13 | 52 | 37 | 6.12% | 86 | 1 | CDP |
Fort Madison is the largest city in Lee County, with a population of 9,900.
Argyle is the smallest city in Lee County, with a population of 52.
There are 13 cities in Lee County, Iowa.