13 cities
| City | County | 2025 Pop. ↓ |
|---|---|---|
| Elk Point | Union County | 2,056 |
| Eagle Butte | Dewey County | 1,275 |
| Elkton | Brookings County | 783 |
| Estelline | Hamlin County | 774 |
| Edgemont | Fall River County | 766 |
| Eureka | McPherson County | 747 |
| Emery | Hanson County | 470 |
| Enemy Swim | Day County | 380 |
| Ethan | Davison County | 358 |
| Egan | Moody County | 249 |
| Evergreen Colony | Faulk County | 93 |
| Eden | Marshall County | 90 |
| Erwin | Kingsbury County | 39 |