Provided herein are a voltage regulator, a memory system having the same and an operation method thereof. The memory system includes a memory device configured to store data, a controller configured to control the memory device, and a voltage regulator configured to supply a pump-out voltage to the memory device or the controller so that the memory device or the controller is operated in the following manner: until a level of the pump-out voltage is increased to a second reference voltage lower than a first reference voltage, the pump-out voltage is output using a clock having a first frequency; when the pump-out voltage exceeds the second reference voltage and does not exceed the first reference voltage, the pump-out voltage is output using a clock having a second frequency lower than the first frequency; and when the pump-out voltage exceeds the first reference voltage, the pump-out voltage is output using the clock having the first frequency.