Over the past three decades, micropumps have been intensively interested to handle and to carry small and precise volumes of liquid in many fields of modern industry. Especially, smart actuator based diaphragm micropumps have received considerable attention because of its simple structure and operation precisely. However, hysteresis phenomenon in the smart actuator is the barrier which prevents the system functioning correctly. This study deals with a mitigation strategy of the hysteresis effects for a typical dielectric electro-active polymer actuator based diaphragm micropump in order to improve the performance of the micropump. Firstly, the forward and inverse hysteresis models are designed and optimized to describe the rate-dependent hysteresis behavior of the actuation system. The model-based control method is then developed and validated to drive the system precisely at high frequencies. Finally, experiments have been conducted to demonstrate the effectiveness of the control strategy in a real application. As a result, the hysteresis behaviors of the smart actuator are effectively compensated at the frequencies up to 1Hz and a maximum time average flow rate of 1.443 mL/min and maximum backpressure of 833.5 Pa at room temperature are recorded.