The relationship between blood selenium level and estimated glomerular filtration rate (eGFR) had been explored in previous studies. However, there are few studies about the correlation between blood selenium level and eGFR in the elderly population. This study was undertaken to investigate the relationship between blood selenium level and eGFR in the aged. The present study was a cross-sectional study and used the National Health and Nutrition Examination Survey (NHANES) 2011–2018 dataset. We investigated the association between blood selenium level and eGFR among participants aged 60 years or older. Totally, 4423 participants were enrolled, and the average age was 69.7 ± 6.9 years old. The means of blood selenium level and eGFR were 192.9 ± 29.5 ug/L and 74.1 ± 19.9 mL/min/1.73 m2, respectively. After adjusting potential confounders (age, gender, body mass index, ethnicity, marital status, education, family income to poverty ratio, smoking, hypertension, and diabetes mellitus), non-linear relationship was detected between blood selenium level and eGFR, whose inflection point was 202 ug/L. The effect sizes (β) and the confidence intervals on the left and right sides of inflection point were 0.07 (0.04 to 0.11) and 0.01 (− 0.02 to 0.04), respectively. In addition, subgroup analysis showed that blood selenium level was positively associated with eGFR, and the test for interactions was not statistically significant in various subgroups. In conclusion, the relationship between blood selenium level and eGFR is non-linear. Blood selenium level is positively related with eGFR when blood selenium level is less than 202 ug/L.