| City | County | 2026 Pop. ↓ |
|---|---|---|
| Elk Point | Union County | 2,061 |
| Eagle Butte | Dewey County | 1,273 |
| Elkton | Brookings County | 808 |
| Estelline | Hamlin County | 802 |
| Edgemont | Fall River County | 779 |
| Eureka | McPherson County | 765 |
| Emery | Hanson County | 463 |
| Ethan | Davison County | 363 |
| Enemy Swim | Day County | 358 |
| Egan | Moody County | 253 |
| Eden | Marshall County | 91 |
| Evergreen Colony | Faulk County | 73 |
| Erwin | Kingsbury County | 41 |