Children in homeless families have high levels of adversity and are at risk for behavior problems and chronic health conditions, however little is known about the relationship between cognitive-emotional self-regulation and health among school-aged homeless children. Children (n = 86; mean age 10.5) living in shelters were assessed for health, family stress/adversity, emotional-behavioral regulation, nonverbal intellectual abilities, and executive function. Vision problems were the most prevalent health condition, followed by chronic respiratory conditions. Cumulative risk, child executive function, and self-regulation problems in children were uniquely related to child physical health. Homeless children experience problems with cognitive, emotional, and behavioral regulation as well as physical health, occurring in a context of high psychosocial risk. Several aspects of children’s self-regulation predict physical health in 9- to 11-year-old homeless children. Health promotion efforts in homeless families should address individual differences in children’s self-regulation as a resilience factor.