The A-6F Intruder was to have been an advanced version of the A-6E, initially known as the A-6E Upgrade. A contract was issued in July 1984, and it was anticipated that the A-6F would be the principal medium attack aircraft in the Fleet in the 1990s. The A-6E Upgrade was to have been virtually a new design, using most of the components of the A-6E but with a new radar, a digital avionics suite, improved engines, the epoxy/composite Boeing wing, and additional weapons stations.

The plane was to have been powered by a pair of General Electric F404-GE-400D turbofans, which were to be smokeless. An third offensive weapons rack was to be added underneath each wing. A new Norden synthetic aperture radar (sometimes known as AN/APQ-173) was to be fitted, and the aircraft was to be capable of carrying the AIM-120A AMRAAM air-to-air missile, which would have given the Intruder an air-to-air capability. The cockpit instrumentation was to be wholly new, with digital instruments being added and multifunction displays provided that were all driven by an AYX-14 computer. The AN/APN-153 Doppler radar was to be replaced by a Collins GPS system. The AN/ALQ-165 Airborne Self-Protection Jammer (ASPJ) was to be fitted. Externally, the A-6F would differ by having an additional dorsal scoop for cooling air. Five full-scale development A-6Fs were ordered. They were diverted from a batch of A-6Es (BuNos 162183/162187), and were known as "Intruder II". They were fitted with Grumman metal wings, since the Boeing composite wings were not yet ready. BuNo 163183 was the aerodynamic and propulsion test vehicle and flew for the first time on August 26, 1987, with Harry Hentx and Dave Goulette at the controls. BuNo 162184 followed on November 23. 162185 was the Digital Systems Development aircraft and was used as the test bed for the AN/APQ-173 radar and other advanced avionics systems, and flew for the first time on August 22, 1988. However, by this time, the A-6F project had been cancelled, and the last two A-6Fs had already been mothballed without being flown. Budgetary constraints were cited as the reason for the cancellation, but the real reason was probably the existence of the Advanced Tactical Aircraft (ATA) stealth attack aircraft project which was currently under development as the A-12 and which was still secret at the time. Unfortunately, the A-12 project was itself cancelled by Secretary of Defense Dick Cheney on January 7, 1991. Mismanagement and delays were cited as the reasons.