Previous findings assessing the relationship between high-density lipoprotein cholesterol (HDL-c) and kidney function have demonstrated contradictory results including positive, negative, and U-shaped relationships. Many prior studies in this area have been conducted in healthy populations, but few have considered the influence of metabolic health status. In the present study, a cross-sectional analysis was conducted using complex survey sample weighting in the assessment of 6455 subjects from the 2013–2018 National Health and Nutrition Examination Surveys (NHANES), representative of 94,993,502 United States citizens. Subjects were classified as metabolically healthy or unhealthy and linear regression analyses were performed to evaluate the influence of HDL-c on estimated glomerular filtration rate (eGFR). HDL-c was found to be negatively associated with eGFR in the metabolically healthy, unhealthy, and combined groups (B = −0.16, p < 0.0001, B = −0.21, p < 0.0001, and B = −0.05, p = 0.0211, respectively). This relationship persisted after adjustment for confounding variables (B = −0.24, p < 0.0001, B = −0.17, p < 0.001, and B = −0.18, p < 0.0001, respectively). The relationship between HDL-c and eGFR was found to be a negative linear association, rather than a U-shaped association, and it persisted in all models tested, despite statistical adjustment for confounding variables. After controlling the samples for outliers, the negative relationship between HDL-c and eGFR was attenuated in the healthy and total groups but remained significant in the MetS group, indicating a stronger relationship between HDL-c and eGFR in those with poorer health.