Background and Objectives: There are few population-based studies on the academic achievement of children with specific congenital anomalies. In this study, we aimed to evaluate the academic achievements of children born with major congenital anomalies compared to children without major congenital anomalies and whether educational achievements are associated with sociodemographic factors. Methods: We performed a population-based study including 401544 children in Finland, graduates of the compulsory school who applied to secondary education. We used health data from the Finnish Register of Congenital Malformations for children born from 1995 to 2002 who had a recorded major congenital anomaly linked with education data from the Finnish Ministry of Education and Culture. We used a generalised linear regression to compare the mean grade differences of children with major congenital anomalies and ‘All anomalies’ subgroup, included children with major congenital anomalies, chromosomal syndromes, and multiple anomalies, with reference children. Results: Children with major congenital anomalies were significantly less likely to apply for further education than reference children (OR, 4.13; 95% CI, 3.92-4.36). For most congenital anomalies studied, children born with congenital anomalies had academic achievements similar to the reference children. For all anomalies subgroup, children with congenital anomalies were at a higher risk of academic underachievement than reference children. Among children with congenital anomalies, male sex, lower maternal educational levels and younger maternal age were associated with significantly lower academic achievement. Conclusions:Most studied congenital anomalies were not associated with lower educational achievements for children who applied for further education. Nevertheless, the grade means were significantly lower in all children with major congenital anomalies that included non-isolated anomalies and for children with selected isolated anomalies. A continuous need for efforts to improve educational outcomes in children with major congenital anomalies while considering sociodemographic background is apparent.