- Eagle
- Empire
- Elrod
- Erskine
- Evergreen Colony
- Eagle Butte
- Edgemont
- Egan
- Emery
- Elk Point
- Eden
- Elkton
- Erwin
- Eureka
- Estelline
- Ethan
- Elbon
- Elevenmile Corner
- Epiphany
- Echo Island (historical)
- Esmond
- Elmore
- Englewood
- Eagle Island
- East Sioux Falls
- El Rancho Acres
- Ellis
- Ellis Corner
- Erickson Subdivision
- Ellsworth Air Force Base