Background: The global coronavirus disease-2019 (COVID-19) pandemic has infected a large subset of women in the reproductive age-group, but the effect of COVID-19 infection on menstruation is still unclear. This study outlines the influence of COVID-19 infection on the menstrual cycle. Methods: Women in the reproductive age-group, admitted with COVID-19 infection were followed up with a structured telephonic interview. Women with previously regular menstrual cycles were included in the study. The questions included severity of COVID-19 infection, details of menstrual cycle before and after the infection, and COVID-related stress recorded by Perceived Stress Scale-10. Results: Data from 350 women with COVID-19 infection were presented. Moreover, 59.1% (n = 207) of women reported a change in their menstrual cycles. About 43.7% (n = 153) noted changes in the volume of flow with 78.4% (n = 120/153) experiencing less flow. Irregular menstrual cycles were reported by 37.1% (n = 130) women, 50.8% (n = 66/130), experienced infrequent menstruation, with delay varying from 45 to 90 days, and 13.8% (n = 18/130) of these women also experienced intermenstrual spotting. Most of these women recovered, and only 17.1% continue to have irregular menstrual cycles even after 1 year of COVID infection. Moreover, 34.28% (n = 120) reported worsening of premenstrual symptoms, and 22.44% (n = 55) reported worsening of dysmenorrhea after the COVID-19 infection. The stress score was not significantly associated with the severity of COVID-19 infection (p >0.05). Social factors like concern about health of other family members, quarantine, and isolation were the biggest contributors to stress. Conclusion: COVID-19 infection and associated stress can influence normal menstruation. Clinical significance: The findings of this study outline the short- and long-term effects of COVID-19 infection on menstruation. This information can be used to reassure the patients and will be helpful in counseling to allay their fears related to altered menstrual cycles after the COVID-19 infection.