This pilot study evaluated the effectiveness of delivering a new cognitive behavioural intervention package ‘Emotion-Based Social Skills Training (EBSST) for Children with Autism Spectrum Disorder (ASD) and Mild Intellectual Disability (ASD + MID)’ in schools. Fourteen school counsellors nominated 75 children (aged 7–13 years) with ASD + MID to receive 16 sessions of EBSST in groups of 3–8 children in their schools. Parent and teacher pre-post ratings of emotional competence (Emotions Development Questionnaire), social skills (Social Skills Improvement System Rating Scales) and mental health (Developmental Behaviour Checklist) were collected. Forty-three children received 16 sessions of EBSST and 32 children were allocated to the 9-month waitlist control group. Teachers and parents also received six EBSST training sessions in separate groups at school. Significant improvements in parent and teacher ratings of emotional competence were found at posttreatment among children in the EBSST group relative to controls; however, the results were not significant after the Bonferroni adjustment. Small to medium effect sizes were found. No difference in untrained social skills or mental health was observed. This study provides preliminary support for the utility of EBSST in teaching emotional competence skills for children with ASD + MID in schools and provides valuable pilot data for future research.