The influence of socioeconomic (SES) inequalities on brain and cognitive development is a hotly debated topic. However, previous studies have not considered that genetic factors overlap with SES. Here we showed, for the first time, that SES and EduYears-PGS (a score from thousands of genetic markers for educational attainment) have independent associations with both cognition and global cortical surface area in adolescents. EduYears-PGS also had a localized association in the brain: the intraparietal sulcus, a region related to non-verbal intelligence. In contrast, SES had global, but not regional, associations, and these persisted throughout adolescence. This suggests that the influence of SES inequalities is widespread -a result that opposes the current paradigm and can help inform policies in education.