Background: Children with autism spectrum disorder (ASD) and intellectual disability (ID) are an understudied population whose school inclusion is challenging. Methods: We assessed the effects of "Developmental and Sequenced one-to-one Educational Intervention" (DS1-EI), a ten-hour-per-week adapted instruction programme for five- to nine-year-old children with ASD and ID treated in outpatient health care institutions. A single-blind multisite randomized controlled trial was conducted to compare DS1-EI given for three years with treatment as usual (TAU)(trial registration numbers: ANSM130282B-31 (April 16, 2013) and ACTRN12616000592448). The primary outcome was the change in the psycho-educational profile (PEP). Secondary variables included the Childhood Autism Rating Scale (CARS), Autism Diagnostic Interview-Revised (ADI-R), Vineland Adaptive Behaviour Scale-II (VABS-II), Children's Global Assessment Scale (CGAS) and annual assessment of educational achievement. Statistical analyses used linear mixed models. Findings: Seventy-two participants with severe ASD and ID were recruited. Intention-to-treat and per-protocol analyses showed no significant group*time interaction for the PEP, CARS, ADI-R, VABS-II and CGAS but a significant effect for educational achievement with a better improvement in the DS1-EI group. At the 36-month time point, more DS1-EI children were included in mainstream classrooms. Additional analyses using multivariate models taking into account moderating variables at the baseline (e.g., Developmental Quotient) confirmed that DS1-EI had a significant effect on educational outcomes. Interpretation: DS1-EI did not improve communication or social skills in children with ASD and ID compared with TAU. However, DS1-EI enhanced school skills in four domains (language, mathematics, inter modality, and school autonomy) favouring inclusion in mainstream classrooms more than TAU. Providing such adapted instruction is feasible and should be encouraged.