This study explores whether the association between living in a single-parent household and children’s educational outcomes differs by migration background through comparing natives with first- and second-generation migrant pupils from different areas of origin. While there is strong evidence of an educational gap between migrant and native pupils in Western countries—and particularly in Italy—the interaction with family structure has been under-investigated. We suggest that native children have more socioeconomic resources to lose as a consequence of parental breakups, and thus may experience more negative consequences from living in a single-parent household compared to migrant children, who tend to have poorer educational outcomes regardless of family disruptions. Moreover, for migrant children, family disruption could result from parents’ migratory project (transnationalism) rather than separation or divorce, thus not necessarily implying parental conflict and a deteriorating family environment. Empirical analyses of data from the ISTAT ‘Integration of the Second Generation’ survey (2015) show that native Italian pupils from single-parent households in lower secondary schools are more strongly penalised in terms of grades, and less likely to aspire to the most prestigious upper secondary tracks when compared to second- and, especially, first-generation children. Indeed, the latter have been found to experience virtually no negative consequences from parental absence. Contrary to expectations, we found no substantial differences in the non-intact penalty based on the reason for parental absence (transnationalism vs divorce), nor by migrants’ area of origin.