A car that can accelerate quickly is of no use on the racetrack unless it can also slow down quickly. The braking system on the F50 is up to the task, yet it is relatively simple. There is no servo assist, as the engineers felt that the size of the brakes made it unnecessary. There is also no ABS (Antilock Brake System) even though they are almost standard equipment on lower priced cars. It should be pointed out that ABS is typically not found on race cars, as a trained driver can effectively control braking without electronic assist. According to the Ferrari web page, "The smoothness with which the system cuts in convinced technicians that an anti-wheel lock system was not necessary."

As reported by Car and Driver in the January 1997 issue, the F50s brakes are not impressive. They were difficult to control (easily locked up, not the most efficient way to slow down) and managed to stop the car from 70 mph in 176 feet, longer than many lesser production cars.