A pulse counting apparatus operating at a low power and an operation method thereof are provided. The pulse counting apparatus includes a pulse counter configured to count a number of pulses inputted from outside of the pulse counting apparatus and generate an interrupt signal; a timer unit configured to generate a wake-up signal according to a preset time; a real time clock (RTC) configured to serve as a clock of the pulse counter and the timer unit; and a processor configured to switch from a sleep mode to an active mode when the interrupt signal or the wake-up signal is generated.