IntroductionData on child functioning and disability are important for public policy development which aimed at reducing child disability prevalence and strengthening the provision of appropriate and timely health care services. This study reports the prevalence of functional difficulty in Malaysian children aged 2–17 years and its associated sociodemographic factors and epilepsy.MethodsData on children aged 2–17 years (n = 4576) were generated from the National Health and Morbidity Survey (NHMS) 2019, a population-based cross-sectional survey. Functional difficulty in children was assessed using the United Nations Children’s Fund (UNICEF)/Washington Group on Disability Statistics (WG) Child Functioning Module (CFM). The questionnaires were administered to the parents or guardians of the children via face-to-face interviews. Functional difficulty, defined as having difficulty in at least one domain, was examined for its prevalence and associations with sociodemographic variables and the epilepsy variable in children using descriptive analysis and multiple logistic regression.ResultsThe overall prevalence of functional difficulty among children aged 2–17 years was 4.7%. Multiple logistic regression analysis revealed that older children, children from households whose heads of household had a lower education level and children who have epilepsy were significantly more likely to experience functional difficulty (p < 0.05). Children of Chinese ethnicity were less likely to experience functional difficulty compared to children of Malay ethnicity.ConclusionsThis study provides baseline findings on the prevalence of functional difficulty among children in Malaysia using nationally representative data. Although the prevalence was relatively low, the information is important for the planning of strategies to improve the development and well-being of children in Malaysia and for achieving the Sustainable Development Goals (SDGs).