Self-regulation refers to the ability to control and modulate behavior, and it can include both emotional and cognitive modulation. Children with neurodevelopmental disorders may show difficulties in self-regulation. The main objective of this study is to improve self-regulation skills in children between 6 and 11 years of age with neurodevelopmental disorders. Methodology: A randomized controlled trial will be conducted with the use of “SR-MRehab: Un colegio emocionante”, based on a non-immersive virtual reality system where virtual objects can be managed by children in a natural way using their hands. Children will be recruited from several schools of Granada (Spain) and they will be randomly allocated to two groups. An assessment will be conducted before and after the intervention and 24 weeks after the end of the intervention process. The experimental group will receive the intervention using virtual reality. The control group will receive a standard self-regulation program. Both interventions will be performed once a week for a total of 10 sessions. Changes in self-regulation, as well as the acceptability of technology with the use of SR-MRehab, will be evaluated. The results will be published and will provide evidence regarding the use of this type of intervention in children with neurodevelopmental disorders. Trial registration: Registered with code NCT04418921.