Background: Gestational age is associated with greater school achievement and variation in newborn metabolic markers. Whether metabolic markers are related to gestational age differences in achievement is unknown. This study examines whether newborn metabolic markers are associated with gestational age differences in performance on standardized school tests. Methods: This retrospective cohort study linked birth certificates of children born in Iowa between 2002 and 2010 to newborn screening records and school tests between 2009 and 2018. The analytical sample includes up to 229,679 children and 973,247 child-grade observations. Regression models estimate the associations between gestational age and 37 newborn metabolic markers with national percentile ranking (NPR) scores on math, reading comprehension, and science tests. Results: An additional gestational week is associated with 0.6 (95% CI: 0.6, 0.7), 0.5 (95% CI: 0.4, 0.5), and 0.4 (95% CI: 0.4, 0.5) higher NPRs on math, reading, and science, respectively. Compared to full term children (37–44 weeks), preterm children (32–36 weeks) have 2.2 (95% CI: −2.6, −1.8), 1.5 (95% CI: −1.9, −1.1), and 1.0 (95% CI: −1.4, −0.7) lower NPRs on math, reading comprehension, and science. Very preterm children (20–31 weeks) have 8.3 (95% CI: −9.4, −7.2), 5.2 (95% CI: −6.2, −4.0), and 4.7 (95% CI: −5.6, −3.8) lower NPRs than full term children on math, reading, and science. Metabolic markers are associated with 27%, 36%, and 45% of gestational age differences in math, reading, and science scores, respectively, and over half of the difference in test scores between preterm or very preterm and full term children. Conclusions: Newborn metabolic markers are strongly related to gestational age differences in school test scores, suggesting that early metabolic differences are important markers of long-term child development.