Sleep problems are common in children and adolescents, particularly those with Neurodevelopmental Disorders. With the changes in daily habits resulting from the COVID-19 pandemic, we have analyzed sleep characteristics, during social isolation, in Brazilian children and adolescents aged between 4 and 12 years with Autism Spectrum Disorder (N = 267), Down Syndrome (N = 74), and typical development (N = 312). The ASD group presented with worse indicators of sleep habits in the Children's Sleep Habits Questionnaire (CSHQ-BR) and fell asleep later during the pandemic. The entire group started fall asleep and waking up later during the pandemic - as well as waking up more often during the night. These results may contribute to parental guidance and sleep habit-related interventions during and after the COVID-19 pandemic.