In this paper, average modeling of a dual-supercapacitor bank, actively balanced by a bidirectional buck-boost converter is presented. In such a system, natural balancing is achieved when the converter is operated in open loop with 50% duty cycle, eliminating the need for measuring the voltage of each storage device. Nevertheless, excessive currents arise even for slight voltage misbalance because of the highly underdamped nature of the system. In order to remedy this drawback, bidirectional pulse-by-pulse inductor current limitation is introduced, which is equivalent to adding a peak-current-mode-like control loop to the system. Since the duty cycle never exceeds 50%, compensation ramp is not required to maintain stability. On the other hand, while the uncontrolled system dynamics is linear, introducing the current limit mechanism turns the closed loop dynamics into a nonlinear one, burdening the analysis task and thus calling for suitable average model to perform fast simulations for system analysis. Dynamical equations of the system are developed in order to derive the switching-cycle-averaged model. Simulations support the presented findings.