Changing the physical environment of healthcare facilities can positively impact patient outcomes. Virtual reality (VR) offers the potential to understand how healthcare environment design impacts users’ perception, particularly among those with brain injuries like stroke, an area with limited research. In this study, our objective was to forge a new pathway in healthcare environment research by developing a comprehensive, six-module ‘user-centered’ design decision support approach, utilizing VR technology. This innovative method integrated patient engagement, architectural design principles, BIM prototyping, and a sophisticated VR user interface to produce realistic and immersive healthcare scenarios. Forty-four stroke survivors participated, experiencing 32 VR scenarios of in-patient bedrooms, followed by interactive in-VR questions and semi-structured interviews. The results of the approach proved to be comparatively efficient and feasible, provided a high level of immersion and presence for the participants, and effectively elicited extremely rich quantifiable response data, which revealed distinct environmental preferences. Our novel approach to understanding end-user responses to stroke rehabilitation architecture demonstrates potential to inform user-centered evidence-based design decisions in healthcare, to improve user experiences and health outcomes in other healthcare populations and environments.