This empirical cross-sectional study explored the effect of chronotypes on classroom behaviour. One hundred and forty young Portuguese children, from 1st to 4th grades, were examined regarding their chronotype and disruptive behaviours occurring in the classroom. Three groups of chronotypes (i.e., morning, intermediate and evening) were identified. The Chronotype Questionnaire for Children evaluated the chronotype of children, and the Conners Scale - reduced version for teachers (self-report) identified the frequency of the following behaviours in the classroom: psychomotor agitation, inattention, and opposition. Multivariate analysis of variance and analysis of regression parameters showed that morning children are more agitated and impulsive compared to evening peers. Concerning academic achievement, students did not differ in the subjects Portuguese and Mathematics for both semesters when considering chronotype and controlling for covariates such as age and gender. Parental qualifications appeared as an influential covariate for the chronotype effect in disruptive behaviour. This evidence addresses the contributions of school policies and family supervision regarding young children: children have earlier evening chronotypes; chronotypes impact specific disruptive behaviours in the classroom; parents’ education influences the sleep habits and behaviours of children in school; parents and schools need more support and evidence to correctly identify children’ chronotypes, to understand how chronotype and sleep habits affect behaviours in the classroom, and to recognise that more studies should be replicated attending to the contextual factors of health outbreaks and war conflict. With reliable data, this study highlights concerns and novelties for education and psychology.