N-terminal pro-B-type natriuretic peptide (NT-proBNP) is a screening marker for heart failure. A previous study demonstrated the positive association between NT-proBNP level and chronic kidney disease (CKD) incidence in individuals aged ≥65 years in the United States. As no report has described the relationship between NT-proBNP level and CKD incidence in Asian populations, we investigated this in the Japanese population. We followed up 867 participants without CKD, history of cardiovascular disease, and atrial fibrillation from the general population of Ohasama, Japan. We defined CKD as an estimated glomerular filtration rate (eGFR) of <60 mL/min per 1.73 m2 and/or proteinuria. The primary outcome was defined as CKD incidence determined during the annual checkups from 2002 to 2014. In accordance with previous studies, the participants were classified into four groups according to NT-proBNP level (<30.0, 30.0–54.9, 55.0–124.9, and ≥125.0 pg/mL). NT-proBNP was measured by using an electrochemiluminescence immunoassay (Roche Diagnostics, Tokyo, Japan). The Cox proportional hazards model was applied to assess adjusted hazard ratios (HRs) for CKD incidence after adjustment for sex, age, body mass index, current smoking status, alcohol consumption, diabetes mellitus, hypercholesterolemia, history of cardiovascular disease, systolic blood pressure, use of antihypertensive drugs, and eGFR at baseline. The participants’ mean age was 59.1 years, and 587 (67.7%) were women. The median (interquartile range) NT-proBNP level was 41.3 pg/mL (23.5–70.0 pg/mL). During the mean follow-up period of 9.7 years, 177 participants developed CKD. When we used the group with NT-proBNP levels of <30.0 pg/mL as reference, the adjusted HRs (95% confidence interval) for CKD incidence in the 30.0-54.9, 55.0-124.9, and ≥125.0 pg/mL groups were 1.34 (0.90–2.01), 1.25 (0.81–1.92), and 1.83 (1.05–3.18), respectively. Natural log-transformed (ln) NT-proBNP was also associated with the risk of CKD (HR [95% confidence interval] per 1-SD increase in lnNT-proBNP (1.30 [1.05–1.61]). Although we performed the stratification analyses according to age, sex, baseline eGFR, use of hypertensive medication, or hypertension for the risk of CKD, no significant interactions were observed between these factors and lnNT-proBNP for the risk for CKD (interaction P ≥ 0.33). The lowest HR per 1-SD increase in lnNT-proBNP was observed in the participants aged <65 years (HR [95% confidence interval] per 1-SD increase in lnNT-proBNP: 1.06 [0.75–1.49]). The present study demonstrated for the first time the association between NT-proBNP level and elevated risk of CKD in an Asian population. The participants with NT-proBNP levels of ≥125.0 pg/mL had a higher CKD risk than those with NT-proBNP levels of <30.0 pg/mL in the present study. This suggests that NT-proBNP can be a significant predictor of CKD incidence in Asian populations. NT-proBNP level is enhanced by ventricular wall stretch or volume overload, which is related to venous congestion. Venous congestion results in renal dysfunction. Moreover, elevated NT-proBNP levels suggest the reduced clearance rate caused by subclinical renal dysfunction because renal excretion is the main route of clearance for NT-proBNP. NT-proBNP level is not only a screening marker for heart failure but also a predictive indicator of kidney prognosis.