A klystron is an important vacuum device which is useful in medical linear accelerators because it amplifies the radio-frequency (RF) signals required to produce high-energy particle beams. The properties of the nonlinear input and output dynamics in the klystron circuit arouse distortion in various types of parameters pertaining to the beam voltage, beam current, RF power, and operating frequency from unpredictable external factors. Therefore, low-level RF (LLRF) control systems can facilitate the regulation of the output of the klystron to a desired level. Low-level RF control system of the klystron is designed to stabilize the applied voltage and control the resonance frequency of the cavity of the klystron. In this work, an infallible low-level RF control system, the most suitable for a klystron, is designed to use a beam monitoring and an interlock system with components that include an isolator and a phase shifter. Moreover, with regard to pulse distortion at the flap top at the RF output power, the stability of the RF power pulse at the flap top part was improved somewhat by a variable inductor which controlled the inside of the pulse modulator. In this LLRF control experiment, the pulse modulator generated 140kV-95A and succeeded in generating RF output power of 2.856GHz-6MW level of an S-band klystron. During this process, the efficiency of the RF power was approximately 42∼45% and the pulse repetition rate was 10 Hz. The flattop pulse width was measured and found to be 1 µs.