Prolonged or excessive stress negatively affects learning, behavior and health across the lifespan. To alleviate adverse effects of stress in school children, stressors should be reduced, and support and effective interventions provided. Animal-assisted interventions (AAI) have shown beneficial effects on health and wellbeing, however, robust knowledge on stress mediation in children is lacking. Despite this, AAIs are increasingly employed in settings world-wide, including schools, to reduce stress and support learning and wellbeing. This study is the first randomized controlled trial to investigate dog-assisted interventions as a mediator of stress in school children with and without special educational needs (SEN) over the school term. Interventions were carried out individually and in small groups twice a week for 20 minutes over the course of 4 weeks. We compared physiological changes in salivary cortisol in a dog intervention group with a relaxation intervention group and a no treatment control group. We compared cortisol level means before and after the 4 weeks of interventions in all children as well as acute cortisol in mainstream school children. Dog interventions lead to significantly lower stress in children with and without special educational needs compared to their peers in relaxation or no treatment control groups. In neurotypical children, those in the dog interventions showed no baseline stress level increases over the school term. In addition, acute cortisol levels evidenced significant stress reduction following the interventions. In contrast, the no treatment control group showed significant rises in baseline cortisol levels from beginning to end of school term. Increases also occurred in the relaxation intervention group. Children with SEN showed significantly decreased cortisol levels after dog group interventions. No changes occurred in the relaxation or no treatment control groups. These findings provide crucial evidence that dog interventions can successfully attenuate stress levels in school children with important implications for AAI implementation, learning and wellbeing.