Background: Coronavirus disease-2019 (COVID-19) has claimed innumerous lives globally resulting in increased stress affecting woman's menstrual, sexual, and mental health, an area of significant concern. The study was aimed to understand the effect of COVID-19 severity on menstrual and mental health. Method: A cross-sectional survey using a closed-ended questionnaire was conducted on COVID-19 positive women of reproductive age (18–45 years), admitted at School of Medical Sciences and Research, Greater Noida, during the period of April 1, 2021, to May 31, 2021. One-hundred and thirteen patients were enrolled to evaluate any change in a menstrual pattern along with alteration in sleep and sexual drive. Depression Anxiety Stress Scale-21 was used to assess mental health. Results were analyzed using the Chi-square test. Results: Nearly, 52.2% of patients reported changes in their menstrual patterns. Change in cycle length was observed in 37.8% of patients, 18% of cases reported heavy or decreased flow while 16.2% of patients had prolonged or short cycles. Patients with moderate-to-severe disease had statistically increased incidence of infrequent cycles, scanty flow, and short cycles and significantly correlated with increased levels of depression, anxiety, and stress. Conclusion: This study highlights the implication of COVID-19 severity on emotional and menstrual disturbances, an aspect which is least addressed and discussed. It also emphasized the need for more frequent post-COVID counseling sessions to improve women's health.