Abnormal menstrual flow is a common concern among young women, especially in academically demanding environments. Despite growing awareness of the impact of nutrition and body composition on reproductive health, there remains a scarcity of localized data, particularly in sub-Saharan Africa, exploring how anthropometric indices correlate with menstrual disturbances. To investigate the relationship between anthropometric variables Body Mass Index (BMI), waist circumference, waist-to-hip ratio (WHR), and body fat percentage and abnormal menstrual flow among female students in the College of Medicine, Ambrose Alli University. A cross-sectional descriptive study was conducted among 408 female medical undergraduates selected using multistage random sampling. Data were collected via a validated self-administered questionnaire and anthropometric measurements. Descriptive statistics, Pearson’s correlation, logistic regression, and ROC analyses were performed using SPSS v25, with significance set at p < 0.05. The prevalence of AMF was 68.9%, with menorrhagia (31.4%) being most common. Over 30% of respondents had elevated body fat, and 25% were overweight. Positive correlations were observed between BMI, waist circumference, WHR, body fat %, and specific AMF types (particularly menorrhagia and polymenorrhea). Logistic regression revealed waist circumference >88 cm and body fat ≥30% as strong independent predictors. ROC analysis indicated body fat % had the highest diagnostic accuracy (AUC = 0.81), followed by waist circumference (AUC = 0.77). Anthropometric measures especially body fat percentage and central adiposity are significantly associated with abnormal menstrual flow. These findings highlight the need for routine body composition screening and menstrual health education in university health services.