An electronic thermostat control system may include a control duty determination portion outputting PWM duty signal for controlling the coolant temperature according to a coolant temperature, a rising rate of the coolant temperature, an engine speed, a load and a vehicle speed, a driving portion applying a time condition to the PWM duty signal output by the control duty determination portion for controlling outputting interval, and a fault diagnosis portion diagnosing operations of the electronic thermostat by analyzing the signals output by the driving portion and changes of the coolant temperature.