Fuselage
The fuselage of the Harrier aft of the cockpit section is dominated by the need to house the Pegasus engine. This is the one area that has changed least over the life of the Harrier, although in detail it has been constantly refined. The most obvious example of refinement are the twin lateral air intakes. Mounted just aft of the cockpit, these have to provide air to the engine with minimum distortion, whether flying backwards at 50 knots or diving at supersonic speed. This has led to a constant process of re-design, although the basic features of large diameter, short length and semi-circular section have remained constant.

Aft of the intakes the Pegasus engine takes up most of the centre fuselage. The four exhaust nozzles are attached to the engine via four circular cutouts in the fuselage side. The fuselage cross section is basically a boat-like U shape in this area, with a large opening above the engine where the wing and engine access panels are attached. Fore and aft of the engine are the lower-fuselage mounting points for the forward and main undercarriage units, with a ventral stores pylon and mounting points for gun pods or strakes between them. Fuel is carried in the intake walls, between the front and rear nozzle cutouts and aft of the rear (hot) engine ducts. Forward this rear fuel tank is the demineralised water tank.

The rear fuselage houses an avionics bay with two lateral access doors. Aft of this is a bay housing electrical and conditioning equipment, while the front hinged airbrake is mounted underneath the avionics bay. The fin and tailplane assemblies are mounted at the rear of the fuselage, with the former having an S shaped leading edge with an aft mounted rudder. The all-moving tailplane features sharp anhedral, being mounted at the same level as the wing. The outer sections of the tailplane interact with the local air flow to provide positive longitudinal stability. The inner sections are washed by airflow strongly influenced by the engine exhaust, so their angle of attack varies little with air speed and aircraft angle of attack.