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Background: Low levels of physical fitness are associated with low physical and mental health. The aims of this study were to assess the health-related physical fitness of children with intellectual disability (ID), and study the association of physical activity and motor development with physical fitness. Methods: One hundred and twenty-eight children with moderate to severe ID (83 boys; age 2–18 years) visiting specialised day programme centres engaged in field-based physical fitness tests (body composition, muscular strength, muscular endurance, and cardiorespiratory fitness). Scores were compared to reference values, and with linear regression analysis the association between the fitness outcomes and physical activity and motor development was studied. Results: High rates of overweight (23–25%) and obesity (10–15%) were found. A majority of the participants (71–91%) scored below reference values for muscular strength, endurance, and cardiorespiratory fitness tests. Physical activity and motor development were positively associated with scores on several fitness test (β = 0.27–0.44; p Conclusions: Children with moderate to severe ID visiting specialised day programme centres have strikingly low physical fitness levels. Policies and interventions to increase the physical fitness for this specific group of children are urgently needed, in which increasing physical activity and motor skills are expected to be effective components.Implications for rehabilitationStrikingly low levels of physical fitness were seen in children and adolescents with moderate to severe intellectual disabilities.This vulnerable group is in need of appropriate interventions to increase their physical fitness levels.Increasing the physical activity is a potential component in these interventions.Improving motor development will most likely lead to improved physical fitness as well. Strikingly low levels of physical fitness were seen in children and adolescents with moderate to severe intellectual disabilities. This vulnerable group is in need of appropriate interventions to increase their physical fitness levels. Increasing the physical activity is a potential component in these interventions. Improving motor development will most likely lead to improved physical fitness as well.