This paper focuses on VR systems for radiotherapy setup training and it proposes a new web-based VR system that supports VR goggles for radiotherapy setup training modified for its see-through mode. The authors have already developed several web-based VR systems that support VR goggles for radiotherapy setup training and clarified that the systems are useful by the user evaluations. Although a single trainee mode is available in one of the systems, usually two trainees collaboratively do the training using it. In the two trainees’ mode, each trainee cannot see the other trainee because this web-based VR system is a complete VR application supporting VR googles. This causes a problem that inhibits natural communication between the two trainees. To solve this problem, the authors newly added a see-through mode to the system. In this paper, the authors introduce the already developed web-based VR systems for radiotherapy setup training and explain how the see-through mode was added to one of them, and also show user evaluation results about the see-through mode.