Background: Elevated levels of proprotein convertase subtilisin/kexin type 9 (PCSK9) have been reported to be related to dyslipidemia, including patients with kidney dysfunction. However, its association with estimated glomerular filtration rate (eGFR) in individuals with normal serum creatinine (SCr) has not been determined. Methods: A total of 2,089 subjects with normal SCr and without lipid-lowering treatment were consecutively enrolled in this study. Plasma PCSK9 levels were measured by ELISA kit and eGFR was evaluated by the Chronic Kidney Disease Epidemiology Collaboration equation. Subjects were divided into a normal eGFR group (n = 1,205, ≥90 mL/min/1.73 m2) and a decreased eGFR group (n = 884, < 90 mL/min/1.73 m2). Baseline characteristics and laboratory findings were compared between the two groups. Spearman’s correlation and linear regression were performed to determine the association between PCSK9 and eGFR. Results: No significant difference in PCSK9 levels was found between the normal eGFR group and the decreased eGFR group (236.84 ± 67.87 vs. 239.98 ± 68.72 ng/mL, p = 0.303). In Spearman’s correlation and multivariable linear regression analysis, no association of PCSK9 levels with eGFR was detected in the total cohort (r = –0.039, p = 0.079; adjusted β = –0.013, p = 0.630). This result remained the same in the subgroups of normal eGFR (r = –0.038, p = 0.190; adjusted β = –0.031, p = 0.367) and decreased eGFR (r = –0.054, p = 0.109; adjusted β = –0.034, p = 0.319). Conclusion: In this single-center study with moderate sample size, the data showed no relationship of PCSK9 levels with normal or decreased eGFR in untreated patients with normal SCr, suggesting that further studies may be needed to understand the relationship between PCSK9 and lipid disorder in different stage of kidney dysfunction.