This study aimed to investigate the relationship between chronotype preference/sleep problems and symptom severity of children with Autism spectrum disorder (ASD) during the confinement and social isolation of the COVID-19 outbreak. This study included 46 drug-naive children aged 4–17 y diagnosed with ASD. The Autism Behavior Checklist (AuBC), Children’s Sleep Habits Questionnaire (CSHQ), and Children’s chronotype questionnaire (CCQ) were filled out before and at the end of the COVID-19 mandated home confinement by the children’s parents. Children with ASD during the home confinement reported higher chronotype scores, i.e., eveningness chronotype, sleep problems, and autism symptom scores compared to the normal non-hone confinement state. The chronotype score and sleep problems of children with ASD during the home confinement period varied according to the AuBC score. The sleep problems of the children with ASD during the home confinement period mediated the relationship between chronotype score and severity of autism symptoms. It is essential to validate the role of the mediator effect of sleep problems and chronotype in larger samples of children with ASD with restricted to home confinement during the pandemic period. If sleep problems can be controlled with parental education, pharmacotherapy, and psychotherapeutic interventions, the impact on children with ASD of home confinement can be reduced.