In a variable valve actuation system of an internal combustion engine employing a variable valve actuator capable of variably adjusting at least intake valve closure timing depending on engine operating conditions, a processor of a control unit is programmed to phase-advance the intake valve closure timing to a predetermined timing value after a piston top dead center position and before a piston bottom dead center position on intake stroke during at least one of an engine starting period and an engine stopping period. The variable valve actuator includes a biasing device by which the intake valve closure timing is permanently biased toward the predetermined timing value.