One of the biggest challenges with species conservation is collecting accurate and efficient information on population sizes, especially from species that are difficult to count. Bats worldwide are declining due to disease, habitat destruction, and climate change, and many species lack reliable population information to guide management decisions. Current approaches for estimating population sizes of bats in densely occupied colonies are time-intensive, may negatively impact the population due to disturbance, and/or have low accuracy. Research-based video tracking options are rarely used by conservation or management agencies for animal counting due to the perceived training and elevated operating costs. In this paper, we present BatCount, a free software program created in direct consultation with end-users designed to automatically count bats emerging from cave roosts (historical populations 20,000-250,000) with a streamlined and user-friendly interface. We report on the software package and provide performance metrics for different recording habitat conditions. Our analysis demonstrates that BatCount is an efficient and reliable option for counting bats in flight, with performance hundreds of times faster than manual counting, and has important implications for range- and species-wide population monitoring. Furthermore, this software can be extended to count any organisms moving across a camera including birds, mammals, fish or insects.