COVID-19 related lockdowns changed our life. Studies report that young women are more susceptible to lockdown-induced adverse effects and stress. As stress and menstrual cycle are associated, we hypothesized that menstrual cycle length might change during lockdown. We examined menstrual cycle length, and sleep-wake behaviors during lockdown in Israel. Participants were 97 women in their fertile years who used Tempdrop fertility sensor™ to track cycles. Data were collected before, during and after lockdown in Israel. Our main finding is that lockdown was associated with changes in menstrual cycle length of most participants, with either increased of decreased length. Changes were reversed when lockdown was terminated. Sleep duration increased during lockdown but we found no relationship between sleep and menstrual cycle. We suggest these findings contribute to the understanding of the relationship between stress, sleep, and menstrual cycle. Further studies should explore the sources for differential effects in sub-groups of women.