In this paper, we propose a new strategy for electrolyte flow rate control in Vanadium Redox Flow Batteries. The keystone of our approach is a novel methodology for determination of optimal reference voltage and robust feedback controller design that provides the desired transient and steady state battery performance. In addition, we introduce a hierarchical scheme of the general battery control system that significantly simplifies classification of battery control tasks and gives guidelines for multistage controller design. The research considers a kilowatt class VRFB system operating in a wide range of loading currents (20–180 A). The proposed control algorithm allows reference trajectory tracking with high accuracy (average error less than 0.0005%), yet providing the required battery performance at twice lower flow rates as compared to the existing solutions, and thus, decreasing pump energy consumption by a factor of 3. As a result, the proposed method can be used for flow rate regulation in practical VRFB systems ensuring their stable and efficient operation under dynamic loading conditions.