Virtual reality (VR) exergaming has emerged as a promising approach to tackle sedentary behavior by merging exercise and gameplay within a virtual environment. This concept promotes increased physical activity while engaging users in immersive gaming experiences. The immersive quality of VR exergaming is associated with the psychological state of ‘flow,’ where users become deeply engaged and driven in their actions. However, empirically measuring and quantifying the flow experience has remained challenging. The present study assessed the relationship between flow and heart rate variability (HRV) in VR exergaming, extending its scope to evaluate associations with heart rate (HR), stress, cognitive workload (CWL), and cybersickness in exergaming and action gaming contexts. This investigation involved 24 participants (Mage = 21.37 years; SD = 2.18; Females = 38%) immersing in a VR exergame (Beat Saber) and an action game (Superhot VR) for approximately 45 min. Alongside analyzing HRV components and the flow, the participants’ user experience regarding CWL and susceptibility to cybersickness is also assessed. The outcomes of this study not only emphasize the significance of VR exergaming but also offer insights into optimizing its potential. By bridging the gaps in understanding the psychophysiological facets of the flow experience, the findings have implications for the future design and VR exergaming interventions to enhance physical activity engagement.