- Eagle
- Eagle Butte
- Eagle Island
- Eakin
- East Sioux Falls
- Echo Island (historical)
- Eden
- Edgemont
- Egan
- El Rancho Acres
- Elbon
- Elevenmile Corner
- Elk Point
- Elkton
- Ellis
- Ellis Corner
- Ellsworth AFB
- Ellsworth Air Force Base
- Elm Springs
- Elmore
- Elrod
- Emery
- Emmet
- Empire
- Englewood
- Enning
- Epiphany
- Erickson Subdivision
- Erskine
- Erwin