Background: Menstrual health reflects overall physiological well-being, yet academic stress significantly disrupts hypothalamic-pituitary-gonadal axis functioning among medical trainees. Despite extensive literature on medical student burnout, a critical empirical gap remains regarding how cohort-wise stress variations map onto specific menstrual parameters within Southeast Asian Islamic university settings. Objective: This study evaluated the relationship between self-reported stress levels and menstrual cycle characteristics—including regularity, duration, and dysmenorrhea severity—among 133 female preclinical medical students (Classes of 2021–2024) at Universitas Muhammadiyah Prof. Dr. Hamka. Methods: Utilizing a quantitative, analytical cross-sectional design with stratified random sampling, primary data were gathered mid-semester using the Perceived Stress Scale (PSS-10), Medical Student Stressor Questionnaire (MSSQ), and FIGO-aligned tracking tools. Hypotheses were evaluated using Chi-Square ( ) tests of independence and multivariate ordinal logistic regression adjusting for age and Body Mass Index. Findings: Overall, 33% ( ) of participants exhibited irregular menstrual cycles, and 16% ( ) reported severe to very severe stress. Chi-Square analysis demonstrated a statistically significant relationship between elevated stress severity and menstrual irregularity ( ). Menstrual irregularity increased progressively from 26% in moderate stress to 63% in severe stress and 67% in very severe stress cases. Significance: These empirical findings substantiate neuroendocrine models of stress-induced reproductive suppression. Practically, they highlight the necessity for university health services to implement targeted mental health counseling, institutional stress-management programs, and routine menstrual health screening for female medical undergraduates.