The association between statin use and fractures has been investigated by several cohort and case–control studies, with inconsistent results, but no case–crossover study has been conducted. This case–crossover study aimed to analyze the association between statin use and fragility fractures in a large older cohort using the National Database of Health Insurance Claims and Specific Health Checkups of Japan. In this study, 446,101 patients aged ≥65 years in Japan who sustained fragility fractures from May 2013 to September 2014 were evaluated. Statin use was compared between the case window (3 days just before the date of the fragility fracture) and three control windows (31–33, 34–36, and 37–39 days before the fragility fracture), and the association between statin use and the occurrence of fragility fractures was estimated using a conditional logistic regression model with 1:3 matching of cases to controls. The adjusted odds ratio for the association between statin use and fragility fractures was 0.86 (95% confidence interval 0.83–0.89). Stratified analyses showed a tendency for a decreased risk of fractures with statin use; females (versus males), very old (versus old) individuals, and those with fractures in the vertebrae (versus proximal humerus, distal radius, or femoral neck) had substantially decreased risks of fractures. The results suggest a decreased risk of fragility fractures associated with statin use in older Japanese individuals, but further studies are needed.