The MH-47E has been used by U.S. Army Special Operations. Beginning with the E-model prototype manufactured in 1991, there were a total of 26 Special Operations Aircraft produced. All aircraft were assigned to 2–160th SOAR(A) "Nightstalkers", home based at Fort Campbell Kentucky. E models were conversions from existing CH-47C model airframes. The MH-47E has similar capabilities as the MH-47D, but includes an increased fuel capacity similar to the CH-47SD and terrain following/terrain avoidance radar.

This aircraft can be equipped with up to 3 pintle mounted medium machine guns (1 on loading ramp and 2 at shoulder windows), generally 7.62 mm (0.308 in) M240/FN MAG machine guns.

The shoulder windows can also carry the Dillen Aero M134 Gatling gun. One such example can be seen on the left of the aircraft.