The production of mosquitoes for control programs or basic research is facilitated by the standardization of rearing conditions allowing the daily manipulation of thousands of individuals. It is crucial to develop mechanical or electronic systems for controlling the density of mosquitoes at each development stage with the aim of reducing costs, time, and human errors. We present herein an automatic mosquito counter using a recirculating water system allowing rapid and reliable counting of pupae without detectable increased mortality. Using Aedes albopictus pupae, we determined the density of pupae and the time of counting for which the device is most accurate, and evaluated the time saved using this device. Lastly, we discuss how this mosquito pupae counter can be useful in small-scale or mass-rearing contexts enabling a number of applications for research purposes as well as operational mosquito control programs.