Abstract Introduction The risk of postoperative sequelae and in-hospital mortality in Japanese patients aged 90 years and older with hip fractures is unexplored. This study aims to use a comprehensive medical claims database in Japan to compare super-elderly patients aged 90 years and older with elderly aged 65–89 and clarify the risk of sequelae and in-hospital mortality in super-elderly patients. Materials and methods We retrospectively analyzed the Diagnosis Procedure Combination (DPC) database for all of Japan from April 2016 to March 2022. Medical records from approximately 1100 DPC-related hospitals were provided with consistent consent during this period. In this study, we focused on super-elderly patients and examined the association with the risk of postoperative pneumonia, pulmonary embolism, myocardial infarction, urinary tract infection, acute renal dysfunction, subsequent cognitive dysfunction, and in-hospital mortality after one-to-one propensity score matching. Results After performing propensity score matching based on sex and comorbidities, 129,953 pairs of patients were identified. These pairs were compared to elderly and super-elderly patients. The results of this study showed that compared with hip fractures in the elderly, hip fractures in the super-elderly were associated with an increased risk of pneumonia, urinary tract infection, acute renal dysfunction, subsequent cognitive dysfunction, and in-hospital mortality after adjustment for confounders. The odds ratio of in-hospital mortality was 2.190 (95% CI 2.062–2.325). Conclusion As it has been shown that super-elderly patients with hip fractures are at greater risk of respiratory and urinary tract infections and increased in-hospital mortality, careful attention should be required for perioperative management.