(1) Background: Epidemiological studies have shown an inverse association between polyphenol intake and cardiovascular risk factors (CVRFs) in adults, but few have provided information about adolescents. The aim of this study was to evaluate the relationship between urinary total polyphenol excretion (TPE) and CVRFs in adolescents. (2) Methods: A cross-sectional study was performed in 1194 Spanish adolescents from the SI! (Salud Integral) program. TPE in urine samples was determined by the Folin–Ciocalteu method, after solid-phase extraction, and categorized into quartiles. The association between TPE and CVRFs was estimated using mixed-effect linear regression and a structural equation model (SEM). (3) Results: Linear regression showed negative associations among the highest quartile of TPE and body fat percentage (B = −1.75, p-value = <0.001), triglycerides (TG) (B = −17.68, p-value = <0.001), total cholesterol (TC) (B = −8.66, p-value = 0.002), and low-density lipoprotein (LDL)-cholesterol (LDL-C) (B = −4.09, p-value = 0.008) in boys, after adjusting for all confounder variables. Negative associations between TPE quartiles and systolic blood pressure (SBP), diastolic blood pressure (DBP), and TC were also found in girls. Moreover, a structural equation model revealed that TPE was directly associated with body composition and blood glucose and indirectly associated with blood pressure, TG, LDL-C, and high-density lipoprotein-cholesterol (HDL-C) in boys. (4) Conclusions: Higher concentrations of TPE were associated with a better profile of cardiovascular health, especially in boys, while in girls, the association was not as strong.