When parents migrate, leaving their children in the origin country, transnational families are formed. Transnational family studies on children who are ‘left behind’ indicate that children suffer psychologically from parental migration. Many of the factors identified as affecting children’s responses to parental migration however are not considered in child psychology and family sociology studies. This study aims to bridge these areas of knowledge by quantitatively investigating the association between transnational families and children’s psychological well-being. It analyzes a survey conducted in three African countries in 2010-11 (Ghana N = 2760; Angola N = 2243; Nigeria N = 2168) amongst pupils of secondary schools. The study compares children in transnational families to those living with their parents in their country of origin. Children’s psychological well-being is measured through the Strengths and Difficulties Questionnaire. Multiple regression analyses reveal that children in transnational families fare worse than their counterparts living with both parents but not in Ghana where living conditions mediate this relationship. This paper also looks at four characteristics of transnational families and finds that specific characteristics of transnational families and country contexts matter: (1) changing caregivers is associated with poorer well-being in all countries; (2) which parent migrates does not make a difference in Ghana, when mothers migrate and fathers are caregivers results in poorer well-being in Nigeria, and both mother’s and father’s migration result in worse outcomes in Angola; (3) the kin relationship of the caregiver is not associated with poorer well-being in Ghana and Nigeria but is in Angola; (4) children with parents who migrate internationally do not show different results than children whose parents migrate nationally in Ghana and Nigeria but in Angola international parental migration is associated with poorer psychological well-being. The study shows that broader characteristics in the population rather than parental migration per se are associated with decreased levels of well-being.