Background: Menstruation and istihadah are closely related to the legality of the worship, meanwhile both of them are uneasy to distinguish. There is an alternative to differentiate two of them by seeing the menstrual cycle in women around or known as menstrual synchrony. Good level of menstrual hygiene and low level of stress are expected to be the factors of menstrual synchrony occurrence. Objective: The purpose of this study is to know the representation of factors related to menstrual synchrony among female students in Pondok Pesantren Krapyak Yogyakarta in 2017. Methods: The design of this study was descriptive observational with cohort approach. The population of this study was female students in Pondok Pesantren Krapyak Yogyakarta who had been staying in the same room for at least 6 months. Seventy-eight subjects were chosen by using stratified proportional sampling technique, consisted of 68 college students and 10 vocational high school students. The data was collected using a menstrual hygiene questionnaire adopted from Yuliana (2010) and DASS 42 questionnaires to calculate the stress level. The assessment of menstrual synchrony used Weller and Weller (1997) calculation. The data was processed with analytic descriptive method. Results: Most subjects have menstrual synchrony (59%) with good level of menstrual hygiene (71,795%), therefore there is no association between menstrual hygiene and menstrual synchrony. The most subjects has low level of stress (35,897%), therefore there is an association between stress level and menstrual synchrony. Conclusion: There is no association between menstrual hygiene and the occurrence of menstrual synchrony and there is an association between stress level and menstrual synchrony occurrence among female students in Pondok Pesantren Krapyak Yogyakarta in 2017.