The Jaguar has an armour protection for critical system components and provision for in-flight refuelling with retractable probe forward of cockpit on starboard side. The windscreen is bullet-proofed against 7.5mm rifle fire.

There are two 30mm Aden guns with 150 rounds of ammunition in the single seater and one 30mm Aden gun on the port side in the trainer. The Jaguar IS carries a variety of unguided ordnance such as the AS-30L ASM, Hunting BL755 CBUs [cluster bomb units], RAF-type slick 454kg bombs, Matra Durandal anti-runway bombs, Lepus 8in reconnaissance flares and Matra F1 and 155 [SNEB] rocket pods.

The Jaguar IS also carries two Magic-II missiles. It can also carry a tactical nuclear payload.