A stump cutter controller and operator presence system includes one or more capacitive sensors in each of the three control levers that control movement of the cutter wheel. A sensor circuit measures changes in the capacitance of the sensors. The controller automatically disengages a drive clutch and applies a brake to the cutter wheel when the controller senses that an operator has left the operating station—which is assumed when the operator has not touched any one of the three control levers of the operator station for a predetermined time. The controller logic is set to allow the clutch to remain engaged during a delay period, of predetermined duration, to permit the operator to move a hand off of one control lever to another control lever. Also, a grace period, of varying duration based on the speed of the cutter wheel, may be provided during which the clutch is reengaged if an operator returns to the controls.