Background: Transcranial magnetic stimulation (TMS) is commonly used for assessing or modulating brain excitability. However, the credibility of TMS outcomes depends on accurate and reliable coil placement during stimulation. Navigated TMS systems can address this issue, but these systems are expensive for routine use in clinical and research environments. Objective: The purpose of this study was to provide a high-quality open source framework for navigated TMS and test its reliability and accuracy using standard TMS procedures. Methods: A navigated TMS system was created using a low-cost 3D camera system (OptiTrack Trio), which communicates with our free and open source software environment programmed using the Unity 3D gaming engine. The environment is user friendly and has functions to allow for a variety of stimulation procedures (e.g., head and coil co-registration, multiple hotspot/grid tracking, intuitive matching, and data logging). The system was then validated using a static mockup of a TMS session. The clinical utility was also evaluated by assessing the repeatability and operator accuracy when collecting motor evoked potential (MEP) data from human subjects. Results: The system was highly reliable and improved coil placement accuracy (position error = 1.2 mm and orientation error = 0.3°) as well as the quality and consistency (ICC >0.95) of MEPs recorded during TMS. Conclusion: These results indicate that the proposed system is a viable tool for reliable coil placement during TMS procedures, and can improve accuracy in locating the coil over a desired hotspot both within and between sessions.