Objective: To estimate the risk of chronic kidney disease in patients with leptospirosis. Methods: All reported (41 890) and later confirmed leptospirosis (1 990) cases from 2010-2020 were traced by universal sampling. 386 Laboratory-confirmed leptospirosis cases were enrolled and 413 age, gender, area, and occupation matched healthy persons were included as controls. Variables including socio-demographic characteristics, medical history, and health-related behaviours were compared between the two groups and association between these variables and reduced estimated glomerular filtration rate (eGFR) was analyzed with multiple linear regression. Results: The median of eGFR was 49.0 (27.0, 75.0) mL/min/1.73 m2 in the cases and 96.0 (72.0, 121.0) mL/min/1.73 m2 in the controls, showing significant differences (P <0.001). Bivariate analysis showed that leptospirosis seropositivitiy, repeat leptospirosis infection, diabetes, male gender, working in field (sun exposure), COVID-19 infection and smoking had statistically significant association with reduced eGFR. Leptospirosis seropositivity had negative effects on eGFR. Multiple linear regression confirmed that leptospirosis seropositivity had negative effects on eGFR (unstandardised p coefficients= −30.86, 95% CI −49.7 to −11.9, P <0.001). Conclusions: Chronic kidney disease is a complex disease with multiple risk factors involved. Exposure to leptospirosis is one of the essential factors in accelerating its progression.