A lack of longitudinal data prevents many countries from estimating dynamic models and, thus, from obtaining valuable evidence for policymaking in the field of education. This is the case of Spain, where recent education reforms have targeted secondary schools, but their design has been based on incomplete information regarding the evolution of student performance and far from robust evidence concerning just when educational inequalities are generated. This paper addresses the absence of longitudinal data required for performing such analyses by using a dynamic model with repeated cross-sectional data. We are able to link the reading competencies of students from the same cohort that participated in two international assessments at different ages (9/10 and 15/16) and so identify when educational gaps—in terms of gender, socio-economic status and place of birth—emerge. Our results suggest that educational inequalities in Spain originate in lower educational levels. These results stress the importance of early intervention for improving performance during the compulsory education and for tackling educational inequalities.