Abstract 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 ( β prenatal = −0.24; β postnatal = −0.28), lower IQ ( β prenatal = −0.20; β postnatal = −0.22), and lower academic achievement ( β prenatal = −0.31; β 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.