Background: Adolescents with intellectual disability have high levels of unrecognized disease and inadequate health screening/promotion which might be addressed by improving health advocacy skills. Methods: A parallel-group cluster randomized controlled trial was conducted to investigate whether a health intervention package, consisting of classroom-based health education, a hand-held health record and a health check, increased carer-reported health advocacy in adolescents with intellectual disabilities. Results: Carers of 388 adolescents responded. Adolescents allocated to receive the health intervention package were significantly more likely to go to the doctor on their own, ask questions and explain their health problems to the doctor without help. Carers reported their adolescent had benefited, gaining increased knowledge and responsibility for their own health. They themselves reported an increase in knowledge and better ability to support the young person. Conclusions: An educational initiative based on the Ask Health Diary led to improved healthcare autonomy for adolescents with intellectual disabilities.