Background <p>Hyperuricemia is increasingly acknowledged as a major public health issue. Current evidence on the effects of urinary phytoestrogen biomarkers on hyperuricemia is limited. Moreover, the potential mediation effect of kidney function was not assessed.</p> Methods <p>This study included 2,793 adults aged 20–79 years from the National Health and Nutrition Examination Surveys (NHANES 2007–2010). We used traditional regression and Bayesian kernel machine regression (BKMR) models to assess the associations of urinary phytoestrogen biomarkers with serum uric acid and hyperuricemia risk, and the mediation effect model to evaluate the role of kidney function in their associations. Estimated glomerular filtration rate (eGFR) was calculated for assessing kidney function.</p> Results <p>Most phytoestrogen biomarkers were inversely associated with serum uric acid and hyperuricemia risk, with mean changes in the estimates ranging from − 0.06 to -0.12&#xa0;mg/dl and odds ratios ranging from 0.80 to 0.90. The BKMR model demonstrated that higher urinary concentrations of phytoestrogen mixtures were associated with lower serum uric acid and hyperuricemia risk, and identified that equol (EQU) and enterolactone (ENT) were the two most important contributors to the overall inverse associations. The BKMR model further confirmed that EQU and ENT were independently associated with lower serum uric acid and hyperuricemia risk. Causal mediation analysis indicated eGFR mediated the associations of EQU and ENT with hyperuricemia risk, with the proportion of mediation ranging from 9.64 to 11.60% (all <i>P</i> &lt; 0.05), respectively.</p> Conclusions <p>Urinary phytoestrogen biomarkers were inversely associated with serum uric acid levels and the risk of hyperuricemia, with EQU and ENT identified as the major contributing metabolites. These findings provide preliminary evidence that renal function may partially mediate the associations of EQU and ENT with uric acid concentrations and hyperuricemia risk.</p>