Early life stress (ELS) is associated with lower IQ and academic achievement; however, it remains unclear whether it additionally explains their discrepancy. In 2,401 children (54% girls, 30.2% migration background) from the population-based study Generation R Study, latent factors of prenatal and postnatal (age 0-10) ELS were estimated, and IQ-achievement discrepancy (age 12) was quantified as variance in academic achievement not explained by IQ. ELS was prospectively associated with larger IQ-achievement discrepancy ([beta][subscript prenatal] = -0.24; [beta][subscript postnatal] = -0.28), lower IQ ([beta][subscript prenatal] = -0.20; [beta][subscript postnatal] = -0.22), and lower academic achievement ([beta][subscript prenatal] = -0.31; [beta][subscript postnatal] = -0.36). Associations were stronger for latent ELS than for specific ELS domains. Results point to ELS as a potential prevention target to improve academic potential.