Introduction: Children with CHARGE syndrome often show delays in balance and motor skills due to multisensory impairments. Research also suggests that children with CHARGE syndrome have fewer opportunities to engage in physical activity. However, little research has examined the relationship among all of these variables. Thus, the purpose of this study was to examine the relationship between balance, motor skills, and physical activity. Methods: Participants consisted of 37 children with CHARGE syndrome aged 3-16 years who could walk independently. Parents of each child with CHARGE syndrome completed a demographics questionnaire and the Physical Activity Questionnaire for Children or Adolescents. Their child completed the Mini-BEST balance test and five motor skills (run, jump, slide, kick, and throw) from the Test of Gross Motor Development II. Results: Results indicate that anticipatory control had significant positive correlations with all five motor skills, sensory orientation with three motor skills, and reactive postural control and dynamic gait with two motor skills. Running was the only variable that had a significant positive correlation with physical activity. Discussion: The findings indicate that balance, especially anticipatory control, plays an important role in fundamental motor skills of children with CHARGE syndrome. There is also a strong connection between physical activity and running competence for this population; however, since this is based on a correlational analysis, the direction of the relationship is unclear. Implications for practitioners: Physical education teachers should work with students with CHARGE syndrome on increasing balance and motor skill performance to give them the competence and confidence to engage in physical activity. Moreover, parents can help by engaging in physical activity with their child at an early age and seeking out additional physical activity opportunities for their child outside of the physical education and school setting.