This paper proposes a DC-link voltage variation compensation method for a 3-level single phase converter for high-speed trains. Since 3-level NPC(Neutral Point Clamped) type converters have the split DC-link causing the inherent problem of voltage fluctuations in the upper and lower capacitors, reducing the voltage difference between the top and bottom capacitors is required. In this paper, compensation time proportional to the voltage difference is added to PWM switching time to solve the voltage variation. The compensation time is obtained by a PI controller. Simulation results demonstrate the validity of the proposed method.