<p>Emotion regulation is essential for psychological development, and mindfulness has shown promise in enhancing emotional, cognitive, and physiological outcomes. However, traditional mindfulness practices can be challenging for children. Virtual reality offers an engaging platform to improve adherence, but its impact on children remains underexplored. This study aimed to assess the effectiveness of a short virtual reality-based mindfulness programme in improving heart rate variability and emotional skills in primary school children.&#xa0;The study involved 127 children aged 9–12&#xa0;years (Years 5 and 6). Heart rate variability, a biomarker of autonomic nervous system activity, was measured across four virtual reality mindfulness sessions, while emotional skills were assessed pre- and post-programme. Results showed significant heart rate variability improvements, with increased high frequency power and physiological coherence indicating enhanced parasympathetic activity, relaxation, and emotional regulation. Although low frequency power decreased significantly after the first session, its interpretation as a marker of sympathetic activity remains controversial, warranting cautious analysis. In addition, the intervention improved emotional skills, particularly emotional clarity and the ability to repair emotions. Younger children (Year 5) showed greater heart rate variability gains than older peers, likely due to higher emotional plasticity during this developmental stage. These findings highlight the potential of virtual reality-based mindfulness to enhance heart rate variability, supporting better physiological and emotional regulation in children. Future research should focus on the long-term effects of these interventions and their broader applicability to promote well-being and resilience in educational and therapeutic settings.</p>