Background Menstrual symptoms may negatively impact pupils' attendance and educational attainment, but rigorous population-based studies are lacking. Methods In a prospective cohort study in England, we assessed associations of self-reported heavy or prolonged bleeding and menstrual pain with school absences and attainment, adjusting for potential confounders. Findings Of 2,698 participants, 36% reported heavy or prolonged bleeding and 56% reported menstrual pain. Heavy or prolonged bleeding was associated with missing 1.7 additional days of school per year (16.58%; 95% CI: 9.43, 24.20), and 48% higher odds of being persistently absent (10% absent or more) (OR 1.48; 95% CI: 1.45, 1.52). Menstrual pain was associated with missing 1.2 additional days of school per year (12.83%; 95% CI: 6.14, 19.95), and 42% higher odds of being persistently absent (OR 1.42; 95% CI: 1.39, 1.46). Heavy or prolonged bleeding was associated with lower scores in compulsory examinations taken at age 16 (-5.7 points; 95% CI: -10.1, -1.2, equating to one lower grade), and with 27% lower odds of achieving five standard passes (OR 0.73; 95% CI: 0.71, 0.75). There was less evidence of an association between menstrual pain and examination scores (-3.14 points; 95% CI: -7.46, 1.17), but menstrual pain was associated with 16% lower odds of achieving five standard passes (OR 0.84; 95 CI: 0.81, 0.86). Interpretation Both heavy or prolonged bleeding and menstrual pain were associated with lower school attendance and educational attainment. Greater research and support are needed to enable girls to achieve their full academic potential. Funding Wellcome Trust and UK Medical Research Council.