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This paper proposes a strategy control for energy storage systems with Electrochemical Capacitors. Electrochemical capacitors are electrochemical devices, which have a similar behavior that conventional capacitor, but with much more capacitance. In this work the electrochemical capacitor is used as an energy storage, with the advantage of its high response. The power converter chosen for this work is a bidirectional boost converter, with the storage element (Electrochemical capacitor) in the low voltage side. Being the high voltage side, of the boost converter, a constant voltage bus. The power converter exposed is a variable structure system (VSS), which has two operation modes. Switching between these modes is governed by a control laws based in a state plane analysis. It is shown that the strategy control is able to be used for bidirectional operation. Experimental results shown a good response with constant and variable disturbance.