In the late 1990s, after the fall of the USSR, many former Warsaw Pact countries were left looking for NATO-compatible fighters, but their political climate (or financial standings) did not allow for the purchase of advanced American-made airframes such as the F-16 or F-15. To capitalise on this, SAAB decided to pursue an "upgraded" variant of their existing JAS39 aircraft which would fill two criteria: to update the Gripens to the same standard as the latest F-16Cs in USAF inventory, giving them the required technology to fulfil the requirements of the Swedish Air Force at the time, and also to add more NATO interoperability and compatibility for more ordnance and mid-air refueling, allowing the new Gripen to easily integrate into many former Warsaw Pact countries which were now joining NATO. This new standard of Gripen, called the JAS39C, would first take to the skies on September 6th, 2002. While this new Gripen failed to attract as many buyers as the venerable F-16, it still found fulfilment for its original task, by helping nations like Hungary and the Czech Republic to replace their outdated MiGs with a more modern, NATO-compatible airframe.

The JAS39C is a Swedish 4th generation fighter introduced in Update "Seek & Destroy" to the top ranks of the Swedish tree. Its main difference over the previous JAS39A is its new avionics and armament, primarily the introduction of a glass cockpit with massive colour displays, replacing the old analogue instruments, and more importantly, the addition of the RB 99 missile, a Swedish licensed copy of the AIM-120A AMRAAM active-radar homing missile. This new missile, which is also compatible with the BOL countermeasures dispenser (giving the Gripen over 700 countermeasures) and a Helmet-Cued Radar Boresight targeting system, coupled with the Gripen's already incredible flight performance thanks to its small profile and lightweight airframe, makes the JAS39C an extremely formidable aircraft.