A fatigue monitoring system is disclosed for use with a machine. The fatigue monitoring system may have an input device configured to generate a first signal indicative of an activity performed by a machine operator, a scanning device configured to generate a second signal indicative of a recognized characteristic of the machine operator, and a warning device. The fatigue monitoring system may also have a controller in communication with the input device, the scanning device, and the warning device. The controller may be configured to determine a time between generations of the first signal, to make a comparison of the recognized characteristic with a threshold characteristic, and to selectively activate the warning device based on the time or the comparison.
