Provided is a method of programming the flash memory device including setting increments of program voltages according to data states expressed as threshold voltage distributions of multi-level memory cells. An Increment Step Pulse Programming (ISPP) clock signal corresponds to a loop clock signal and the increments of the program voltages and is generated in response to program pass/fail information. A default level enable signal is generated by performing a counting operation until reaching the increments of the program voltages, in response to the loop clock signal. An additional level enable signal is generated by performing a counting operation until reaching the increments of the program voltages, in response to the ISPP clock signal. The program voltage is increased by 1 increment, in response to the default level enable signal. The program voltage is increased by 2 increments, in response to the additional level enable signal.