While the association between parental separation and children’s lower educational achievements is a robust finding, the evidence regarding its heterogeneity across social groups is mixed. Some studies show that socioeconomically advantaged families manage to shelter their pupils from the consequences of parental break-up, while others find the opposite. We contribute to this debate and sketch a structural theory of the heterogeneity of the consequences associated to parental separation on children’s educational outcomes. We argue that the separation penalty and its heterogeneity across social backgrounds differ depending on the selectivity of a given educational outcome. In particular, the smallest penalty will be observed for very rare and very common outcomes. The rarity of an educational outcome depends on pupils’ social background, which might produce the observed heterogeneity even if the separation penalty itself is equal across parental social background. We investigate the heterogeneity of the consequences of separation by parents’ education in Spain on two children’s outcomes. One outcome (enrolment in tertiary education) is rare for children in low educated families, while the other (retaking in primary and secondary education) is rare for children in highly educated families. The results show that the penalty associated to parental separation for retaking a year in primary and secondary education is larger for children of low educated mothers. No heterogeneity is found for enrolment in tertiary education.