Background. Disturbances in menstruation such as change in menstrual amount and cycle irregularity have not been listed among the common side effects of coronavirus disease 2019 (COVID-19) vaccines. Recent studies have found COVID-19 vaccination may affect menstruation in women who previously had regular menstrual cycles. However, it rarely causes breakthrough bleeding in the amenorrheic women. Case presentation. We present a 49-year-old woman with panhypopituitarism and secondary amenorrhea of over 16 years duration who had vaginal bleeding and dysmenorrhea after administration of COVID-19 vaccine. Vaginal bleeding appeared at 2 months after the second dose of AstraZeneca COVID-19 vaccine. Laboratory data was significant for low serum FSH level of 1.67 mIU/ml during the menstrual period, and her platelet count was normal. Transvaginal ultrasound revealed thickening of the endometrium (1.55 cm), and no abnormality in the uterus and the adnexa. Dilation and curettage of endometrium was reported stromal endometrial glands in secretory phase and without evident hyperplasia or malignancy. The association of breakthrough bleeding and COVID-19 vaccination in this case can not be excluded. Conclusion. Both mRNA and adenovirus vector COVID-19 vaccines have been reported to affect menstruation, suggesting the vaccine-induced immune response rather than specific vaccine components may be the causative factor. Researches exploring the associations and possible mechanisms of vaccine-induced menstrual abnormalities are ongoing. Vaccine recipients who report changes in menstrual cycle or postmenopausal vaginal bleeding should be managed according to usual clinical guidelines.