Significance The influence of socioeconomic status (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 show 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 nonverbal 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.