An ultrasonic vibration has been superposed on the normal electrode movement to increase the flushing effect during a micro electro-discharge machining (EDM) process. A systematic study on the effects of ultrasonic vibration on the EDM performance for fabricating microholes in Nitinol has been completed. The introduction of ultrasonic vibration to the micro-EDM process has increased the machining efficiency more than 60 times, without significantly increasing the electrode wear. Numerical simulation reveals that the efficiency improvement is attributed to the strong stirring effect caused by ultrasonic vibration, which results in an excellent flushing in the micro-EDM process.