This study describes the synthesis of zinc oxide nanoparticles (ZnO NPs) using a microfluidic system. A continuous and efficient synthetic process was developed based on a microfluidic reactor in which was implemented a time pulsed mixing method that had been optimized using numerical simulations and experimental methods. Numerical simulations revealed that efficient mixing conditions could be obtained over the frequency range 5–15 Hz. This system used ethanol solutions containing 30 mM sodium hydroxide (NaOH) or 10 mM dehydrated zinc acetate (Zn(OAc)₂) under 5 Hz pulsed conditions, which provided the optimal mixing performance conditions. The ZnO NPs prepared using the microfluidic synthetic system or batch-processed system were validated by several analytical methods, including transmission electron microscopy (TEM), energy dispersive X-ray spectrometry (EDS), X-ray diffraction (XRD), UV/VIS NIR and zeta (ζ) potential analysis. Bulk-heterojunction organic photovoltaic cells were fabricated with the synthesized ZnO NPs to investigate the practicability and compared with batch-process synthesized ZnO NPs. The results showed that microfluidic synthesized ZnO NPs had good preservability and stability in working solution and the synthetic microfluidic system provided a low-cost, environmentally friendly approach to the continuous production of ZnO NPs.