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Introduction More than 800 million patients currently have chronic kidney disease (CKD), placing a tremendous burden on both the healthcare and welfare economies. Habitual physical activity in patients with CKD may extend healthy life expectancy without functional disabilities; however, the relationship remains unclear. This study aimed to investigate the impact of habitual physical activity on the association between CKD and long-term nursing care certification.Methods This observational cohort study enrolled participants aged >64 years without long-term care certification based on functional disabilities. Habitual physical activity data were obtained using questionnaires, and 8428 participants were classified into the Kidney Disease Improving Global Outcomes risk categories at baseline: no CKD (n=5717), moderately increased risk (n=1980), high risk (n=542) and very high risk (n=189) groups. The primary outcome was long-term care certification, and HRs were estimated using the no CKD group with habitual physical activity as reference.Results Among the participants with habitual physical activity, very high risk CKD significantly increased the risk of functional disabilities requiring long-term care (HR 1.64, 95% CI 1.04 to 2.58). Meanwhile, non-habitual physical activity significantly increased the risk of functional disabilities with CKD progression, with the HRs for the no CKD, moderately increased risk, high risk and very high risk groups being 1.35 (95% CI 1.16 to 1.57), 1.30 (95% CI 1.07 to 1.58), 1.51 (95% CI 1.16 to 1.96) and 2.30 (95% CI 1.62 to 3.26), respectively.Conclusions CKD progression is related to the risk of developing functional disabilities requiring long-term care. Habitual physical activity can help extend healthy life expectancy and reduce CKD-related welfare burden.