Pupillometry is a popular method because pupil size is easily measured, sensitive to central neural activity, and associated with behavior, cognition, emotion, and perception. Currently, there is no method for online monitoring phases of pupil size fluctuation. We introduce rtPupilPhase - an open source software that automatically detects trends in pupil size in real time, enabling novel implementations of real time pupillometry towards achieving numerous research and translational goals. We validated the performance of rtPupilPhase on human, rodent, and monkey pupil data and propose future applications of real time pupillometry.