A three-dimensional computational model has been developed to investigate the cooling of a microchip by micro-channels in which water is flowing and in which a synthetic jet generator has been installed at the mid-point of the channels. The synthetic jet operates at a fixed frequency and amplitude of the diaphragms while the pressure difference between the ends of the channels is varied. For a microchip with a constant thermal load, when the synthetic jet is not operating, because the flow rate in the channels increases as the pressure difference is raised, as would be expected, the maximum temperature in the wafer is reduced as the pressure difference is increased. As the result in this steady flow, the maximum temperature in the silicon wafer with a thermal load of 1 MWm-2 is decreased by 11.3 K when the channel pressure difference is raised from 500 Pa to 1500 Pa. It is shown that when the synthetic jet is activated at a constant frequency and amplitude, the flow patterns in the channels are quite different at the two pressure differences. As a consequence, whilst the maximum temperature in the silicon wafer is lowered in each case below that prevailing when the flow is steady, after the 40th cycle of membrane oscillation the reductions in the maximum temperature in the silicon wafer are 9 K and 7.5 K below those in steady flow for with channel pressure differences of 500 Pa and 1500 Pa respectively. It follows that the reduction in temperature caused by a synthetic jet is lessened if the pressure difference between the ends of the channels is significantly increased. Therefore, the channel pressure difference and the synthetic jet parameters are equally important in determining the optimal operating condition.