In mainstream education, the transition from primary to secondary school (‘school transition’) is difficult for children with autism spectrum disorder, being marked by high levels of emotional and behavioural difficulties. The Systemic Transition in Education Programme for Autism Spectrum Disorder (STEP-ASD) is a new, manualised school transition intervention. We investigated its feasibility and efficacy for children diagnosed with autism spectrum disorder (N = 37; mean age = 11.47 years; mean IQ = 85.24) using an unblinded, non-randomised, controlled design. Teachers found the intervention feasible and acceptable. Children receiving STEP-ASD (n = 17) showed a large (Cohen’s d = 0.88) reduction in school-reported emotional and behavioural difficulties, whereas controls (n = 20) showed a slight increase (d = -0.1) (p = 0.010). These encouraging findings suggest the value of STEP-ASD as a low-intensity intervention for reducing problem behaviours and distress in children with autism spectrum disorder as they transition to mainstream secondary school.