Many biomedical applications require the administration of drugs at a precise and preferably programmable rate. The flow rate generated by the peristaltic micropumps used in such applications depends on the actuation sequence. Accordingly, the current study performs an analytical and experimental investigation to determine the correlation between the dynamic response of the diaphragms in the micropump and the actuation sequence. A simple analytical model of a peristaltic micropump is established to analyze the shift in the resonant frequency of the diaphragms caused by the viscous damping effect. The analytical results show that this damping effect increases as the oscillation frequency of the diaphragm increases. A peristaltic micropump with three piezoelectric actuators is fabricated on a silicon substrate and is actuated using 2-, 3-, 4- and 6-phase actuation sequences via a driving system comprising a microprocessor and a phase controller. A series of experiments is conducted using de-ionized water as the working fluid to determine the diaphragm displacement and the flow rates induced by each of the different actuation sequences under phase frequencies ranging from 50 Hz to 1 MHz. The results show that the damping effect of actuation sequences influences diaphragm resonant frequency, which in turn affects the profiles of flow rates.