Synchrony refers to parent–child interactions that are mutually regulated, reciprocal, and harmonious. Synchrony is associated with a variety of positive developmental outcomes but a small literature indicates that children with less synchronous relationships tend to display emotional and behavioral problems. Despite this association, no study to date has observed synchrony among clinical child populations and little is known about the mechanisms underlying the synchrony–child behavior relation. Since strained parent–child relations are often associated with parenting stress and parenting stress increases the risk of child maladjustment we propose that parenting stress mediates the relation between synchrony and child behavior problems. We tested this hypothesis and examined the clinical relevance of synchrony by observing naturalistic play in 19 clinic-referred and 23 non-clinic referred mother–child dyads. Children ranged in age from 6 to 10 years. We found lower synchrony in clinic-referred dyads compared to non-clinic referred dyads and that parenting stress mediated the association between synchrony and child problem behavior. The findings from the current study have implications for the development of emotional and behavioral problems in children as well as for assessment and treatment for child clinic populations.