As normally found on Japanese cars; a minor or mid life change (Kouki in Japanese) occurs halfway through the production cycle. In 1989, halfway through its expected build life, the FC RX-7 saw a multitude of small refinements. Rotary engine technology had had continued its advance in the 3 years. The engines themselves used new lighter, higher compression rotors. The combustion recesses on the rotors were fully machined and chromed for heat control. With the machining, the compression ratios of each of the rotor's combustion chambers as well as rotor weight, could be more closely matched. The side seal thickness was reduced from 1.0 mm to 0.7 mm. The compression ratio for the normally aspirated models jumped to 9.7 and 9.0 for the turbo respectively (up from the 9.4 and 8.5). For both increased emission restrictions and better engine management the engine computer was speed was doubled.

On the normally aspirated (NA) engines the changes allowed the redline to be increased to 8000 RPM. A rotary valve was added between the intake tracks which started opening at 4500 RPM. This variable dynamic intake (VDI) valve enhanced the DEI (Dynamic Effect Intake) by altering the length of the fuel/air mixture path based on engine speed and load. The airflow meter was also changed from the flapper type to a linear type for reduced air resistance and more precise measurement. The oil metering pump was changed from a mechanical pump to an electronic model for more effective control of the lubrication and reduced oil consumption. These engine modifications raised the output of the NA 13B to 160 HP @ 7000 RPM and 140 lb/ft of torque @ 4000 RPM. The power band was effectively widened, giving more usable power at lower RPMs.

The Turbo II received a new turbocharger. Mazda called it the "Completely Independent Twin Scroll". The impeller was fed directly at the exhaust port. The Mazda press release in 1989 said: “This permits the powerful exhaust pulse generated by the opening of the exhaust port to directly hit the turbine blades without interference from the exhaust from the other rotor." This newer design resulted in reduced turbo lag and increased torque. The new electronically controlled wastegate allowed higher boost pressures and quicker response. The modifications resulted in the peak torque smoothed through the 2000 to 5000 RPM band. The horsepower also climbed another 18 ponies to give the revised Turbo II a Mazda claimed total of 200 horse power @ 6500 RPM and 196 lb-ft of torque at 3500 RPM.

The automatic transmission was now electronically controlled with a "hold" mode that allowed the transmission to be shifted manually in the lower three gears. Ball joint mountings were used on the sway bars to reduce noise, harshness, and vibration. Vehicle speed sensitive power steering became standard on the Turbo II, but in the GTU and GTUs normally aspirated models a less accurate and cheaper engine speed sensitive power steering was used (and was eventually phased into the entire line except the Turbo by 91). The fuel tank was increased to 18.5 gallons in all models.

Inside the car, shifting was enhanced by a revised shift rod mechanism, and a shorter shift rod. Leather was used to cover the shift ****, steering wheel, and hand brake, in all models except the GTU (base) model. The seats were re-contoured for better lateral support. The temperature, fuel, voltage, and oil pressure gauges were placed in round recesses rather than the pie wedges that were used previously and a minor revision was made to the instrument surround. The center console radio, shifter and Logicon (climate control) surrounds were slightly re-contoured with a new rubberized material with the Logicon itself getting updated icons for air direction. A new parcel shelf was added that hid items in the "trunk". Controversial motorized seat belts became standard on the coupes in the USA and black became an interior color option with the gray interiors no longer available.

Exterior cosmetic changes included new a body trim strip that now matched the car color. The front bumper was slightly reshaped with the nose cap restyled with the word MAZDA embossed rather than the decal found on the '86-'88 models. On the upper level models integrated 55 watt fog lights were placed above the brake vents in the front bumper. The radiator opening was reshaped. A new slightly larger rear spoiler similar to the one found of the Turbo II and GTU in '88 became standard on all coupes. A slightly more rounded version of the Turbo II Aero mirrors also became standard across all models. On the Turbo II a new front spoiler and integrated side skirts replaced the 88 models Aero kit. And finally new tail lights finished off the exterior body changes. The GTUs and Turbo II received new 16"x7" wheels which were radically lighter than the previous design and licensed from BBS, while new 15"x 6" 5 lug wheels became standard in the base models and the GXL. The convertible retained its ultra lightweight 11 lb 15"x 6.5" BBS wheels.

The former base model, the GX/SE was updated with 5 lug wheels, and was renamed the GTU. While the former GTU/Sport model became the GTUs with a aluminum hood (from the Convertible), a new 4.3 rear end ratio and .762 top gear. The GTUs was designed to be a race ready street car with Air Conditioning and a AM/FM radio the only options. Similar to the series 4 Sport/GS the GTUs also had reduced insulation, 4 piston front brakes and the heavy duty suspension. The Limited Slip Differential found on the Series 4 GXL was dropped on the Series 5 GXL to save weight and costs.

An automatic transmission became available on the Convertible, and ABS became standard on the Turbo II.