The F-14 received its first of many major upgrades in March 1987 with the F-14A Plus (or F-14A+). The F-14A's P&W TF30 engine was upgraded with the GE F110-400. The F-14A+ also received the state-of-the-art ALR 67 Radar Homing and Warning (RHAW) system. Much of the avionics as well as the AWG-9 radar were retained. The F-14A+ was later redesignated F-14B on 1 May 1991. A total of 38 new aircraft were manufactured and 48 F-14A were upgraded into B variants.

The TF30 had been plagued from the start with susceptibility to comressor stalls at high AoA and during rapid throttle transients or above 30,000 ft (9,100 m). The F110 engine provided a significant increase in thrust, producing 27,600 lbf (123 kN) with afterburner. The increased thrust gave the Tomcat a better than 1:1 thrust-to-weight ratio at low fuel quantities. The basic engine thrust without afterburner was powerful enough for carrier launches, further increasing safety. Another benefit was allowing the Tomcat to cruise comfortably above 30,000 ft (9,100 m), which increased its range and survivability. The F-14B arrived in time to participate in Desert Storm.

In the late 1990s, 67 F-14Bs were upgraded to extend airframe life and improve offensive and defensive avionics systems. The modified aircraft became known as F-14B Upgrade or as "Bombcat".

The final variant of the F-14 was the F-14D Super Tomcat. The F-14D variant was first delivered in 1991. The original TF-30 engines were replaced with GE F110-400 engines, similar to the F-14B. The F-14D also included newer digital avionics systems including a glass cockpit and replaced the AWG-9 with the newer AN/APG-71 radar. Other systems included the Airborne Self Protection Jammer (ASPJ), Joint Tactical Information Distribution System (JTIDS), SJU-17(V) Naval Aircrew Common Ejection Seats (NACES) and Infra-red-search and track (IRST).

Although the F-14D was to be the definitive version of the Tomcat, not all fleet units received the D variant. In 1989, Secretary of Defense Dick Cheney refused to approve the purchase of any more F-14D model aircraft for $50 million each and pushed for a $25 million modernization of the F-14 fleet instead. Congress decided not to shut production down and funded 55 aircraft as part of a compromise. A total of 37 new aircraft were completed, and 18 F-14A models were upgraded to D-models, designated F-14D(R) for rebuild. An upgrade to the F-14D's computer software to allow AIM-120 AMRAAM missile capability was planned but was later terminated.

While upgrades had kept the F-14 competitive with modern fighter aircraft technology, Cheney called the F-14 1960s technology. Despite some aggressive proposals from Grumman for a replacement, Cheney planned to replace the F-14 with a fighter that was not manufactured by Grumman. Cheney called the F-14 a "jobs program", and when the F-14 was canceled, an estimated 80,000 jobs of Grumman employees, subcontractors, or support personnel were affected. Starting in 2005, some F-14Ds received th e Rover III upgrade.

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