The Wankel rotary engine offers a greater power density than piston engines, but higher fuel consumption and hydrocarbon emissions, in large part due to poor gas sealing. This paper presents a model for the deformable dynamics of the side seal, which completes a set of modeling tools for the comprehensive assessment of the gas leakage mechanisms in the rotary engine. It is shown that the main leakage mechanisms for the side seals are: (1) opening of the inner flank due to the contact with the trailing corner seal, (2) flow through the gap with the leading corner seal, (3) simultaneous opening of both inner and outer flanks due to body force at high speed, and (4) running face leakage due to nonconformability at high speed. The leakage mechanisms are qualitatively validated at low speed with observed oil patterns on the rotor from laser-induced fluorescence (LIF) experiments. Finally, the predicted total leakage area for all the gas seals ranges from 1.5 mm2/chamber at low speeds to 2 mm2/chamber at high speeds, which is in agreement with the previous experimental studies, and the three gas seal types (side seals, apex seals, and corner seals) each accounts for about 1/3 of the total leakage, with minor variation as a function of speed.