13 cities
| City | County | 2025 Pop. ↓ |
|---|---|---|
| Elk Point | Union County | 2,031 |
| Eagle Butte | Dewey County | 1,213 |
| Edgemont | Fall River County | 790 |
| Elkton | Brookings County | 790 |
| Estelline | Hamlin County | 782 |
| Eureka | McPherson County | 750 |
| Emery | Hanson County | 474 |
| Enemy Swim | Day County | 380 |
| Ethan | Davison County | 361 |
| Egan | Moody County | 249 |
| Evergreen Colony | Faulk County | 93 |
| Eden | Marshall County | 90 |
| Erwin | Kingsbury County | 40 |