Are fly-by-wire fighters protected in AoA? When thinking about fly-by-wire, I always think about civilian aircraft (Dassault Falcon 7X, Airbus A350...) for which protections are implemented to ensure the aircraft stays in its designed flight envelope (load factor limits to avoid overstressing the airframe, AoA limits to avoid stall, bank angle limits to avoid inverted flight...). All these restrictions help maintaining the aircraft in a manageable situation while in flight. Some (e.g. pitch or bank angle limits) are OK for airliners but counterproductive for fighters. Other are clearly applicable to both (e.g. load factor. You don't want to overstress your airframe or risk a G-LOC).

My question concerns AoA protection. For fighters, I imagine this protection can avoid loss of roll control while stalling. Yet, some fighters are able to fly at AoA obviously beyond stall angle (e.g. during a cobra), suggesting this protection is not present.

Do fly-by-wire fighters have an AoA protection? If so does it prevent stall? (I can imagine a protection triggered only if a limit is reached for at least a certain amount of time, or a limit beyond stall angle but not far beyond.) Does it have to be deactivated for manoeuvre such as the cobra (I expect every system to be able to be deactivated on such aircraft)?
Brief answer: Yes, but the protection does not always work.

Most modern fighter aircraft have an AoA limiter. That is different from a stall warning – in case of the McDonnell Douglas F-4 the limit was only 23 degree, below the stall limit. The reason for the limit was the loss of directional stability above 23 degree AoA.

In case of the JAS-39 Gripen the limiter worked in a straight pitch-up but when the pilot repeatedly pitched up during a flight display over Stockholm, the dynamic response overpowered the AoA limiter and the aircraft stalled. It fell like a stone into a public park, miraculously without loss of life.

In another accident the JAS-39 FCS software got confused after the controls could not follow the change in angle of attack quickly enough when one aircraft flew through the wake of another, its adversary in an air combat exercise. This caused the safe limit of 20 degree to be exceeded and the aircraft became uncontrollable.