Abstract Background Regular menstruation is a crucial indicator of comprehensive well-being in adolescents. We aimed to assess risk factors associated with menstrual cycle dysfunction in a population-based cohort of high school students, focusing on academic performance, sports participation, and disordered eating. Methods In 2022, we recruited 1161 female first-year students from 21 diverse high schools in the capital region of Finland. They completed an online survey comprising questions about menstrual cycle, academic achievement, sports involvement, disordered eating and school burnout. Results Of 935 (81%) participants (mean age 16) not using hormonal preparations, 336 (37%) reported irregular menstruation. Adolescents with irregular menstruation showed higher middle school grade point average (GPA) (OR 1.4, 95% CI 1.1-1.8), lower body mass index (OR 2.2, 95% CI 1.3-3.5), and more disordered eating symptoms (OR 2.1, 95% CI 1.4-3.0) than adolescents with regular menstruation. While overall physical activity showed no significant correlation with irregular menstruation, casual exercisers with irregular menstruation exhibited both higher GPAs (OR 1.4, 95% CI 1.4-1.9) and more disordered eating symptoms (OR 2.6, 95% CI 1.6-4.1) than competitive athletes, whereas competitive athletes with irregular menstruation showed higher school burnout scores than casual exercisers but no disordered eating. Conclusions We recommend the use of screening tools to recognize disordered eating and school burnout among female high school students facing menstrual irregularities. Key messages • A third of adolescent females had irregular menstruation. Casual exercisers with irregular menstrual cycle were at risk of eating disorders and competitive athletes at risk of school burnout. • Screening of disordered eating and school burnout among adolescent females facing menstrual irregularities could be beneficial.