Active winglets, with a manually controlled attitude angle, can take advantage of the self-excited force to suppress the flutter tendency of a bridge girder. Previous studies mostly focused on the effectiveness and robustness under long-term closed-loop control. However, the deck-winglet system’s short-term response, due to the memory effect of the aerodynamic force, is of concern. A bridge sectional model with active winglets was developed to investigate this problem. Experiments with different phase shifts between the members of the winglet pair were carried out in a wind tunnel. We found that the influence residue of an instantaneous change of the control pattern lasted about three pitching cycles, indicating that a large control interval was acceptable for practical applications. A theoretical relationship between the control effect and control phase was derived to explain the results of the open-loop control. The system responses under different control intervals were analyzed by the closed-loop control, demonstrating that a large control interval was acceptable if some time-consuming algorithms are used in a practical bridge’s flutter control operation.