: The control and operation of a single-phase 13-level power conditioning system (PCS) for peak power reduction of a high-speed railway substation (HSRS) are proposed. This PCS is a single-phase 3100 V, 2 MVA 13-level H-bridge multi-level inverter structure. It has excellent power quality. It is easy to serialize by voltage. In addition, the DC bus power of each cell inverter is supplied by lithium-ion batteries. The generalized reduction gradient optimization algorithm based on past load pattern is applied to the power management system for peak power reduction of HSRS. The phase detector and power controller for the control of a single-phase PCS based on virtually coordinated axes using an all-pass filter are expected to be robust to external disturbances with fast response characteristics. This study also proposes an adapted select switch (ASS) method that can change the switching depending on the operation state of PCS and the state of charge (SOC) of the battery to minimize battery imbalance by controlling each cell inverter of the H-bridge. The validity of the proposed system was confirmed by PSiM simulation and experiments using a demonstration system of 6 MW PCS and 2.68 MWh batteries at one of Gyeongbu high-speed line substations in Korea.