This paper proposes the design methodology of the voltage controller for a Dual-Active-Bridge (DAB) converter applying the Spread Spectrum Modulation (SSM) to spread EM noises, based on a small-signal model and its analysis. When power electronics devices operate at a fixed switching frequency, high EM noise concentrates on the switching frequency and its harmonics. The SSM is a switching modulation technique that reduces the EM noise by varying the operating frequency to spread the noise distribution according to the frequency domain. When the SSM is applied, the DAB converter has variable switching frequencies. Because the output voltage of the DAB converter depends on the switching frequency, the SSM affects it. Therefore, it is necessary to design a controller based on the small-signal model that considers the frequency variation caused by the SSM. In this paper, using the small-signal model of the DAB converter em-ploying the SSM, the controller for regulating the output voltage is designed, and the converter performance is verified by simulations and experimental measurements with a 3.3 kW prototype converter.