The F-89E was to have been an F-89D re-engined with a pair of 9700 lb.s.t. Allison J71 non-afterburning turbojets. The J71 engines would, it was hoped, give the Scorpion greater power and better fuel consumption, which would result in a much longer range. One F-89C (50-762) was modified as a testbed under the designation XF-89E, and fitted with a pair of 9500 lb.s.t. YJ71-A-3 engines. The air intake was redesigned with a larger capture area and with an additional tip on the upper surface for better high angle attack performance. A pair of large airscoops were fitted underneath each nacelle for cooling purposes. The YF-89E prototype flew for the first time on June 10, 1954. However, the F-89E did not offer much improved performance beyond that of the F-89C/D, and the project was abandoned before anything could reach production. The XF-89E prototype continued to be used as a flying testbed.
The designation F-89E was also applied to a proposed single-seat escort fighter version of the Scorpion. The proposed F-89E was to be powered by a pair of 9100 lb.st. afterburning General Electric J47-GE-21 engines. The wings were enlarged and were fitted with a swept leading edge. The armament consisted of 108 FFARs mounted in a pair of large pods mounted at mid-span on the wings. The main landing gear was stowed inside the pods. The nose was to be altered to carryarmament–alternative arrangements of ten 0.50-inch machine guns, six
20-mm cannon, or six MX-904 rockets were considered. The escort fighter F-89E was projected to have a maximum speed of 688 mph and a combat radius of 1010 miles. The project never got past the design study stage.