Recently, the employment rate of women in Japan has steadily increased. Approximately 80% of women experience menstrual pain and premenstrual syndrome (PMS). These symptoms decrease a woman’s quality of life and her work productivity, leading to an economic loss. This cross-sectional study of 321 healthy Japanese women aged 20–39 years aimed to clarify the lifestyle-related factors or nutrient intake that might cause menstrual pain. The participants underwent body composition measurements and completed meal survey sheets and lifestyle questionnaires, including menstrual status, exercise, sleep and breakfast consumption. Based on the questionnaire results, participants were divided into two groups according to the severity of menstrual pain, namely, heavy and light. Chi-square and Wilcoxon signed-rank sum tests were used to compare the severity of menstrual pain in the two groups. In the heavy group, the intake of animal proteins, including fish, vitamin D and vitamin B12, was significantly lower (p< 0.05), as was the frequency of breakfast consumption and bathing (p< 0.05). The rate of PMS symptoms was significantly higher in the heavy group (p< 0.05). This study suggests that a lack of animal protein, the accompanying vitamins and fatty acids, and the frequency of breakfast or bathing are associated with the severity of menstrual pain.