Background: Pain interferes with the functioning of typical children, but no study has examined its effect on children with pre-existing intellectual disabilities (ID). Methods: Caregivers of 63 children observed their children for 2-h periods and recorded in 1-week diaries: pain presence, cause, intensity and duration. Caregivers also recorded the children's performance of pre-existing skills during each period. Proportion of skills displayed when pain was present and absent was compared. Fifty caregivers completed a second set of observations when pain was present and absent. Results: Comparison of the first set of observations indicated children displayed significantly more abilities (64%) when pain-free (Pain-Free Day 1), than when pain was present (54%; Pain Day 1). Children displayed 64% of their possible abilities during Pain-Free Day 2, but only 53% during Pain Day 2. Pain impacted all areas of function (communication, daily living, social and motor skills). Children's physical and demographic characteristics did not moderate the impact of pain on function, but functioning of children with more severe ID was most impacted by pain. Conclusions: Children perform fewer adaptive skills when pain is present. This could affect long-term functioning as well, through reduced practice of skills.