Objective To explore the relationship between physical activity, sedentary time, and irregular menstrual cycles in women of reproductive age. Methods Conducted between April and June 2024 using convenience sampling, the cross-sectional study assessed physical activity and sedentary time through the International Physical Activity Questionnaire-Short Form (IPAQ-SF), while menstrual cycles was self-reported. Associations were analyzed using logistic regression and restricted cubic spline models, with E-values calculated to assess the influence of potential unmeasured confounders. Results Among 1,259 participants averaging 25 years old, moderate physical activity was linked to a 40% lower risk of irregular menstrual cycles compared to low activity (OR = 0.60, 95% CI: 0.44, 0.81), and high physical activity was associated with a 46% reduced risk (OR = 0.54, 95% CI: 0.37, 0.79), after adjusting for all covariates. Meeting World Health Organization guidelines for moderate-to-vigorous activity was associated with a 36% decreased risk (OR = 0.64, 95% CI: 0.48, 0.85). Sedentary time showed no significant link to irregular menstrual cycles. E-value analysis suggested that unmeasured confounders would need a moderate association strength (1.8–2.1) with both exposure and outcome to negate these findings. The risk of irregular menstrual cycles began to rise when weekly total metabolic equivalents exceeded roughly 3,185 MET-minutes. Conclusion Moderate to high levels of physical activity are inversely related to irregular menstrual cycles in reproductive-aged women, though excessively high activity may increase risk. Ensuring adequate physical activity appears more crucial than merely reducing sedentary behavior.