Due to controversary over whether it actually produced the claimed 320 hp in 1999 models, Ford didn’t produce the Cobra in 2000. Instead it reworked the Cobra to actually produce 320 hp. Likely to fill the gap and help hush the controversy, Ford produced a Cobra R. Only 300 were produced. it featured a 5.4 L V8 that produced 385 hp but lacked a radio, air conditioning, or a back seat. On the exterior, a special hood, front air dam, wheels, and side exhausts.

Other than the Cobra not being produced and the Cobra R, the 2000 Mustang lineup was unchanged from 1999.