Background: Previous studies have shown that obesity is a risk factor for estimated glomerular filtration rate (eGFR) decline and chronic kidney disease (CKD). However, the relationship between fat mass directly measured by bioimpedance analysis and eGFR is not well known. Methods: We analyzed 21,859 participants without CKD at baseline who underwent two health checkups at a 5-year interval during 2002-2009. Fat mass was measured by Inbody 3.0 (Biospace, Seoul, Korea). eGFR decline was defined as eGFR <60 ml/min/1.73 m2 at second checkup. Logistic regression analysis was used to analyze factors related to eGFR decline. Results: Participants were divided into tertiles according to their fat mass change over 5 years: lower tertile (n = 7,042; <-0.7 kg), middle tertile (n = 7,478; -0.7 to 1.2 kg) and higher tertile (n = 7,339; >1.2 kg). After 5 years, 246 cases of eGFR decline were observed. Multivariate logistic analysis revealed that age (OR 1.03, 95% CI 1.02-1.05, p < 0.001), diabetes mellitus (OR 2.04, 95% CI 1.22-3.40, p = 0.007), baseline eGFR (OR 0.80, 95% CI 0.78-0.83, p < 0.001) and higher tertile of fat mass change (OR 1.58, 95% CI 1.16-2.13, p = 0.003) were associated with eGFR decline after adjustment for sex, hypertension, dyslipidemia, cardiovascular disease, smoking status, body mass index, and high-density lipoprotein cholesterol level. Conclusions: Fat mass gain over 5 years was independently associated with eGFR decline to <60 ml/min/1.73 m2 in a relatively healthy Korean population. This finding suggests that lifestyle changes to prevent fat mass gain could be protective against the development of CKD.