This study examined the association between the estimated glomerular filtration rate (eGFR) and disability incidence according to sedentary time in community-dwelling Japanese older adults. This prospective cohort study sampled 5,104 community-dwelling older adults (≥65 years) enrolled in a health promotion study in a general population. The participants (n = 4,457; ≥65 years) were monitored for inclusion in the long-term care insurance system for 4 years. This study used blood samples to assess eGFR. Cox proportional regression analysis was used to determine predictors of disability. In total, 461 participants (10.3%) became newly certified as needing long-term care insurance services. Cox regression models were adjusted for multiple confounders: eGFR < 45 ml/min/1.73 m2 (hazard ratio = 1.741, 95% confidence interval [1.193–2.539]) and eGFR < 45 ml/min/1.73 m2 with high sedentary time (≥8 hr) (hazard ratio = 4.367, 95% confidence interval [2.021–9.438]) remained significantly associated with disability incidence. Our findings suggest that in the case of chronic kidney disease, the disability incidence rate may be affected by sedentary time.