Objective: The purpose of the present study was to investigate the prevalence of eating disorders and their relevant factors in Japanese women. Methods: Anonymous self-administered questionnaire surveys of 3023 working women aged 20–39 were conducted during health checkups in Tokyo, Nagoya, Osaka, and Fukuoka in 2012. Eating disorders were assessed using Eating Attitudes Test-26 (EAT-26). The factors related to EAT-26 scores ≥20 were analyzed by multiple logistic regression. Results: The prevalences of eating disorders among the participants with EAT-26 scores ≥20 were 2.4% [95% confidence interval (95% CI): 1.8–2.9%] of all the participating women aged 20–39, 3.4% (95% CI: 2.5%–4.3%) of women in their 20s, and 1.2% (95% CI: 0.6%–1.8%) of women in their 30s. Logistic regression analysis showed that EAT-26 scores of ≥20 were associated with the following variables: perceived ideal BMI ≤17.5 kg/m² (OR: 4.55, 95% CI: 2.08–9.93), change in body weight in the previous six months (OR: 2.83, 95% CI: 1.61–4.95), being 20–29 years of age (OR: 2.64, 95% CI: 1.42–4.89), and the perception of being fat (OR=2.54, 95% CI: 1.24–5.18). Conclusions: The prevalence of eating disorders with EAT-26 scores ≥20 was 2.4% (95% CI: 1.8%–2.9%) among Japanese working women aged 20–39. EAT-26 scores ≥20 were most closely associated with a perceived ideal BMI of ≤17.5 kg/m². Eating disorders may be more prevalent among women who want to lose weight to achieve a BMI of ≤17.5 kg/m², and these women should be carefully monitored.