Many general purpose engines, such as the ones used in construction machines, operate in environments with excessive amounts of airborne dust, and are thereby equipped with a cyclone air cleaner so that they can remove as much dust from contaminated air streams in the engine. However, the compact general purpose engine is mainly a single-cylinder type, and the intake flow pulsates. Since the centrifugal action of the cyclone air cleaner under the intake pulsation changes according to the pulsation, it is difficult to enhance the dust separation performance. In this study, we aimed to determine a cyclone air cleaner factor with high purification performance even under the intake pulsation conditions of a general purpose engine. We have designed an ideal geometry for the cyclone air cleaner, which centrifugally separates dust during inhaling and discharges the centrifuged dust using positive pressure due to pulsation. A numerical calculation of the flow under the intake pulsation of this cyclone air cleaner was carried out, and the separation and discharge functions were analyzed. Accordingly, it was confirmed that although the swirling speed inside the cyclone air cleaner depended on pulsation, it demonstrated purification performance even under an intake pulsation by the dust discharge function. We have also found a method to operate the discharge function at the instant when the separation function is the strongest.