An electronic active lock pin control method may include checking whether a default position of a lock pin is present, determining whether the checked default position of the lock pin is due to lock pin parking or limphome, entering the default position of the lock pin into an active mode at a time of the lock pin default position by the lock pin parking, while entering the default position of the lock pin into a passive mode at a time of the lock pin default position by the limphome, and performing a phase control mode to track the middle phase type CVVT target value after the passive mode or the active mode.