Behavioral Problems (BPs) in Pakistani Left-behind adolescents (LBA) remain under-investigated. Previous studies exposed that family functioning had a profound effect on LBAs’ behavioral problems, but the mediating and moderating mechanisms that cause this effect are under-studied. In this study, we planned to investigate factors linked with BPs in a large sample of LBAs. This study conferred how left-behind adolescents (LBA) perception of family functioning (FF) influenced their behavioral problems (BPs) through self-esteem (SE). This study also explicated how mother nurturance (MN) affected family functioning direct effects on self-esteem, as well as family functioning indirect effects on BPs via self-esteem. The data for the present research was collected from 400 LBAs in three waves from Rawalpindi and Rawalakot, Pakistan. The results indicates that family functioning had a significant negative predictive impact on BPs. Furthermore, SE acts as a mediator between family functioning and LBAs’ BPs. The outcomes further explicated that mother nurturance has moderating effect on the relationship between family functioning and self-esteem as well as indirect effects on BPs through self-esteem supporting the moderating mediation model. This research offers some innovative implications for practice and research. So, identifying the issues of left-behind adolescents can provide imperative understandings for the development of interventions aiming at the mental health of left-behind adolescents and need to be implemented to improve family functioning in migrant fathers’ family.