This study explored the factors associated with healthcare avoidance behavior for menstrual disorders and menopausal symptoms among women in Japan. Using data from a nationally representative cross-sectional online survey conducted in September 2022, responses from 4,950 women aged 25–59 were analyzed. This study applied binomial logistic regression models specifically to participants who reported having ever felt the need to seek healthcare assistance due to health issues related to menstruation and menopause. We computed adjusted odds ratios for key sociodemographic traits, work environment factors, health literacy, menstrual and menopausal symptoms, and attitudes and understanding regarding women’s health, associated with healthcare avoidance behavior in the past 12 months. As a sensitivity analysis, a regression was performed limited to those who are working. The results showed that 50.6% of respondents recognized the need for healthcare support for menstrual or menopausal health issues, but 22.8% exhibited healthcare avoidance in the past year. Younger and high-income individuals showed higher avoidance rates. Those with diagnosed gynecological conditions and those perceiving menstrual pain as something to endure also displayed increased avoidance tendencies. Women experiencing significant health effects beyond work and those lacking understanding of the purpose of health check-ups were more prone to healthcare avoidance. Our results underscore the importance of implementing strategically tailored health education initiatives, and re-examining societal attitudes concerning women's health, in order to cultivate enhanced healthcare-seeking behaviors among women.