A control system includes a controller. The controller counts the number of driving times of the high pressure fuel pump, which is the number of the reciprocating motions of the plunger based on a crank counter that is counted up at every predetermined crank angle. The controller stores a map in which a top dead center of the plunger is associated with a crank counter value, and store a crank counter value while an engine is stopped as a stop-time counter value. The controller calculates, referring to the map, the number of the crank counter values corresponding to the top dead center of the plunger between a crank counter value and the stop-time counter value, and set a calculated number as the number of driving times.