Objective: Sex-, age-related discrepancies in development of chronic kidney disease (CKD) suggest that sex hormones play important roles in the development of CKD. We aimed to investigate the effect of levonorgestrel intrauterine system (LNG-IUS), one of the progestin-only agents, on the development of CKD. Materials and methods: This retrospective cohort study used claims data from the Korean Health Insurance Review and Assessment Service. The study participants were women aged 30-49 years old who were diagnosed with endometriosis, uterine fibroids, or abnormal uterine bleeding (AUB) between 2014 and 2017. Extended Cox proportional hazards regression models and log-rank tests were performed. Results: A total of 33,822 and 1,193,021 participants from the LNG-IUS and non-LNG-IUS groups, respectively, were included. The incidences of CKD in the LNG-IUS and non-LNG-IUS groups were 40 (0.12 %) and 1953 cases (0.13 %), respectively. In multivariate analysis, LNG-IUS did not associate with increased or decreased risk of CKD: Hazard ratio (HR 0.967, 95 % confidence interval, 0.704-1.328, p = 0.836) after adjusting for calendar year, age, socioeconomic status, regional area, endometriosis, uterine fibroids, AUB, Charlson Comorbidity Index, anemia, autoimmune disease, cardiovascular disease, cerebrovascular disease, chronic pulmonary disease, hypertension, diabetes mellitus, dyslipidemia chronic liver disease, gall bladder, biliary tract, pancreatic disease, neuropathy, obesity, and thyroid disease. The cumulative incidence of CKD between the two groups was not different significantly (log-rank test, 0.9). Conclusion: The LNG-IUS treatment was not associated with increased or decreased risk of CKD. No significant difference was observed in the cumulative incidence of CKD based on the use of the LNG-IUS.