There is no empirical research on the school performance of children who live separated from their parents in sub-Saharan Africa—a major migrant sending region in the world. This study uses survey data from junior and secondary school children and youths in Ghana (N = 2760), Angola (N = 2243) and Nigeria (N = 2168) to examine how different transnational family formations such as internal or international parental absence accompanied by migration or divorce, who is the migrant parent and who is the caregiver, the stability of the caregiving arrangement and remittances relate with the school performance of children who stay behind. School performance is measured through an index of grades in language, mathematics and science. The results show that international parental migration (Ghana), the internal parental migration accompanied by divorce/separation (Nigeria) and migration of both parents (Ghana and Nigeria) are likely predictors for decreased school performance. No effects are observed when parents are abroad and divorced/separated, when only one parent migrates, when children are in a stable care arrangement or when children receive remittances or not. The analyses show that the overall relationship between parental absence and education varies by the transnational dimension being analysed and by context.