A memory device and an operating method thereof are provided. The memory device includes: a plurality of memory strings connected between a bit and source lines, the plurality of memory strings connected to a first select line, a plurality of word lines, and a second select line, which are disposed between the bit line and the source line; a peripheral circuit for programming a selected memory cell included in a selected memory string among the memory strings; and control logic for controlling the peripheral circuit to program the selected memory cell. The control logic controls the peripheral circuit to apply a positive voltage to the bit and source lines, which are connected to an unselected memory string, before a program voltage is applied to a selected word line connected to the selected memory cell, and discharge the word lines and the first and second select lines at different times.