Background: The use of high-sensitive cardiac troponin T (hsTnT) in urine as a marker of cardiac damage in children has not yet been reported. Elimination of cardiac troponins is dependent on renal function; persistently increased serum hsTnT concentrations were observed among individuals with impaired renal function. The aim of this study was to investigate serum and urine hsTnT levels and its correlation in infants and children younger than 24 months of age after cardiac surgery. Methods: This study was conducted on 90 infants and children under 24 months of age who were divided into three groups. The experimental group consisted of patients with intracardiac surgery of ventricular septal defect (VSD), first control group consisted of infants with extracardiac formation of bidirectional cavopulmonary connection (BCPC), and the second control group consisted of healthy children. Troponin T values ​​were determined in serum and urine at five time points: the first sample was taken on the day before cardiac surgery (measure 0) and the other four samples were taken after the surgery; immediately after (measure 1), on the first (measure 2), third (measure 3), and fifth postoperative day (measure 5). The first morning urine was sampled for determining the troponin T in the control group of healthy infants. Results: A positive correlation between troponin T values in serum and urine was found. Urine hsTnT measured preoperatively in children undergoing BCPC surgery was higher (median 7.3 [IQR 6.6–13.3] ng/L) compared to children undergoing VSD surgery (median 6.5 [IQR 4.4–8.9] ng/L) as well as to healthy population (median 5.5 [IQR 5.1–6.7] ng/L). After logarithmic transformation, there was no statistically significant difference in urine hsTnT concentration between the groups at any point of measurement preoperatively or postoperatively. Statistically significant negative correlation was found between serum and urine hsTnT concentrations and glomerular filtration rate estimated by creatinine clearance. Patients who underwent surgical repair of VSD had significantly higher concentrations of troponin T in serum on the first three postoperative measurements compared to those who had BCPC surgery. Conclusions: According to the results of this study, renal function after cardiac surgery appears to have a major effect on the urinary hsTnT concentrations, and we cannot conclude that this is an appropriate marker for the assessment of postoperative myocardial damage in children. Nevertheless, more research is needed to reach a better understanding of the final elimination of cardiac troponins in children.