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Some changes appeared in women’s menstrual cycle after receiving the coronavirus disease 2019 (COVID-19) vaccine, but the information about the pattern and characteristics of these symptoms was unclear. This study was conducted to estimate the prevalence of menstruation change and evaluate the association between COVID-19 vaccination and the occurrence of such disturbance. An online web-based survey was conducted during March–April 2022 that targeted 729 COVID-19 vaccinated women aged between 18 and 45 years in the Jazan region of Kingdom of Saudi Arabia. The tool collected demographic information, psychological data, and COVID-19 post-vaccination side effects. The overall prevalence of menstrual change among the women was 60.9% (95% CI 57.3–64.4). 66.3% and 64.1% of women, respectively, in the age group of 25–34 and 35–45 years were more affected. Most of the detected abnormalities were related to delayed menstruation and changes in pain intensity. Menstrual disturbances that occur after immunization are transient and have no long-term implications. Menstrual disorders are prevalent before vaccination, but there is a considerable increase following vaccination. Because there is no apparent cause for these post-vaccine disturbances, and their effects are difficult to anticipate, it is preferable to warn those concerned and encourage them to learn more about the biological changes causing these problems.