To investigate the prevalence of CSS in a general population. A large-scale cross-sectional study on 21,661 residents (7,531 men, 14,130 women) in a community in Japan was performed. CSS were assessed using Central Sensitization Inventory (CSI-A, B). Participants with a CSI-A score ≥40 was defined as having CSS. Age, sex, district, CSI-B (10 CSS-related diseases), lifestyle, and mental health factors were rated in a self-reported survey. The prevalence of CSS and its relationship with potential factors were examined by sex using descriptive and logistic regression models. The prevalence of CSS was 5.4% (95% Confidence Interval (CI) 5.1 to 5.7) in all participants. It significantly differed between men (3.6%, 95% CI 3.2 to 4.1) and women (6.3%, 95% CI 5.6 to 6.7). A CSI-A score ≥40 correlated with more than one CSI-B disease, exercise habits, sleeping hours per day, perceived stress, and resilience in both men and women. In women, age, ex-smokers, coffee intake (≥1 day per week), and alcohol intake correlated with CSS. The prevalence of CSS was 5.4% in the community examined and was higher in women than in men. CSS-related diseases and many factors correlated with CSS. The present results provide important information for future research on CSS.