Background: It has been suggested that children with intellectual disabilities (ID) have motor problems and higher-order cognitive deficits. The aim of this study was to examine the motor skills and executive functions in school-age children with borderline and mild ID. The second aim was to investigate the relationship between the two performance domains. Methods: Sixty-one children aged between 7 and 12 years diagnosed with borderline ID (33 boys and 28 girls; 71 less than IQ less than 79) and 36 age peers with mild ID (24 boys and 12 girls; 54 less than IQ less than 70) were assessed. Their abilities were compared with those of 97 age- and gender-matched typically developing children. Qualitative motor skills, i.e. locomotor ability and object control, were evaluated with the Test of Gross Motor Development (TGMD-2). Executive functioning (EF), in terms of planning ability, strategic decision-making and problem solving, was gauged with the Tower of London (TOL) task. Results: Compared with the reference group, the full ID cohort scored significantly lower on all assessments. For the locomotor skills, the children with mild ID scored significantly lower than the children with borderline ID, but for the object control skills and the TOL score, no significant differences between the two groups were found. Motor performance and EF correlated positively. At the most complex level, the TOL showed decision time to be a mediator between motor performance and EF: the children with the lower motor scores had significantly shorter decision times and lower EF scores. Analogously, the children with the lower object control scores had longer execution times and lower EF scores. Conclusions: The current results support the notion that besides being impaired in qualitative motor skills intellectually challenged children are also impaired in higher-order executive functions. The deficits in the two domains are interrelated, so early interventions boosting their motor and cognitive development are recommended.