AimConsumption of soy isoflavones reduces the risk of estrogen‐related diseases, such as menopausal symptoms, osteoporosis, and cardiovascular disease. Equol is metabolized from the isoflavone daidzein by intestinal bacteria and has higher bioavailability than other isoflavones. Equol producers are believed to benefit from soybean consumption to a greater extent than non‐producers. Recently, we showed that equol non‐producers were at significant risk of premenstrual syndrome (PMS). Previously, we reported that PMS is a common menstrual problem in female athletes, and almost half of the studied athletes felt a negative effect of premenstrual symptoms on their athletic performance. This study was conducted to evaluate the relation between PMS and equol production status in Japanese collegiate athletes.MethodsThis was a cross‐sectional, observational study that included 88 Japanese female collegiate athletes. Equol production status was determined using urine samples collected after a soy challenge test. The subjects also completed a questionnaire about their premenstrual symptoms and their competitive career.ResultsThe prevalence of equol producers was 29.5% in Japanese collegiate athletes. The athletic performance of 54.5% of athletes was found to suffer in competition or in practice due to premenstrual symptoms. In multivariate analysis, equol non‐producers (odds ratio, 3.34; 95% confidence interval, 1.03–12.20) and restriction of bodyweight (odds ratio, 4.94; 95% confidence interval, 1.47–20.00) were shown to be significant risk factors for poor athletic performance.ConclusionThis study showed a relation between athletic performance and equol production status in Japanese collegiate athletes.