This study examined the influence of physical health and well-being vulnerability on participation in physical activities, and whether motor skill proficiency mediated this relationship. Kindergarten children (n = 260) completed the Test of Gross Motor Development-2 and the Children’s Assessment of Participation and Enjoyment survey. A multivariate analysis of covariance was used to compare the motor skills and participation in physical activities of children in schools classified as more or less vulnerable. We also examined whether motor skill proficiency mediated the relationship between vulnerability status and participation. Children in neighborhoods with higher vulnerability demonstrated lower motor skill proficiency and participation. Object control skill proficiency mediated the relationship between vulnerability and participation. Children from more vulnerable schools started their school career with less developed motor skills and a narrower array of recreation participation. Children in vulnerable neighborhoods need more opportunities to master object controls skills and access recreational activities. Fortunately, motor skill proficiency among children considered ‘at risk’ is amenable to improvement and intervention early in the children’s school career may have a beneficial impact on children’s physical activity at school and beyond the school environment.