Secondary flow in a double-inlet pulse tube refrigerator with a double bypass valve configuration was evaluated to determine the advantage of this configuration in controlling the secondary flow over a conventional single valve configuration. In the double-valve configuration two needle valves was connected in parallel and their respective valve directions were in opposite directions, namely, one valve was directed toward the hot end and the other toward the inlet of the regenerator. The effects of valve configuration on the flow behavior of the secondary flow, on the cooling performance, and on the pressure-volume (work) diagram for gas were investigated. The secondary flow was visualized by using a smoke-wire flow visualization technique, and cooling performance was estimated based on the temperature difference between the hot and cold ends. Results showed that the double-valve configuration allowed the operating conditions of the refrigerator to be optimized to maximize the work and minimize the heat loss by the secondary flow, whereas the single-valve configuration did not leave room for such adjustment. After optimization, however, the singlevalve configuration still showed fairly good performance, comparable to that of the doublevalve configuration.