Studies on children and adults combined suggest higher mortality rates for autistic than other people, but few report mortality rates for autistic children. In addition, past studies may not be representative of the current generation of children diagnosed with autism. We examined mortality in children using data from Scotland’s annual pupil census, linked to National Records of Scotland deaths register, between 2008 and 2015. In total, 9754 (1.2%) of 787,666 pupils had autism. They were more likely to live in neighbourhoods of greater deprivation and receive free school meals. Six autistic pupils died; crude mortality rate 15.8/100,000 person-years (95% CI = 7.1–35.1), compared with 458 other pupils; crude mortality rate 12.5/100,000 person-years (95% CI = 11.4–13.7). The indirectly standardised mortality ratio was 1.1 (95% CI = 0.5–2.5). In the autistic pupils, the most common causes of death were nervous system diseases, for example, epilepsy. Avoidable causes were common. In the comparison group, external causes and cancers were the most common causes of death. We cautiously conclude that mortality in the current generation of autistic children is no higher than for other children, perhaps due to recent widening of criteria for autism spectrum diagnosis, but some deaths could have been avoided by better care.Lay abstractThere are few studies on the deaths of children and young people with autism; some studies on children and adults combined suggest that those with autism may have higher death rates than other people. More children are diagnosed with autism than in the past, suggesting that there are now more children with milder autism who have the diagnosis than in the past, so studies in the past might not apply to the current generation of children and young people diagnosed with autism. We examined the rates of death in children and young people in Scotland using recorded information in Scotland’s annual pupil census, linked to the National Records of Scotland deaths register, between 2008 and 2015. In total, 9754 (1.2%) out of 787,666 pupils had autism. Six pupils with autism died in the study period, compared with 458 other pupils. This was equivalent to 16 per 100,000 for pupils with autism and 13 per 100,000 pupils without autism; hence, the rate of death was very similar. In the pupils with autism, the most common causes of death were diseases of the nervous system, whereas they were from external causes in the comparison pupils. The autism group had some deaths due to epilepsy which might have been prevented by good quality care. We cautiously conclude that the death rate in the current generation of children and young adults with autism is no higher than for other children, but that even in this high-income country, some deaths could be prevented by high quality care.