A method of operating a non-volatile memory device includes selecting a first select transistor from among a plurality of select transistors included in a NAND string, and performing a check operation on a first threshold voltage of the first select transistor. The check operation includes comparing the first threshold voltage with a first lower-limit reference voltage level, and performing a program operation on the first select transistor when the first threshold voltage is lower than the first lower-limit reference voltage level. When the first threshold voltage is equal to or higher than the first lower-limit reference voltage level, the check operation on the first threshold voltage is ended.