The aim of this study was to investigate the effect of Troponin-T levels on the prognosis of neonatal encephalopathy (NE). The study included one hundred and eleven newborns diagnosed with NE and receiving hypothermia treatment. The cases were separated into 2 groups according to the SARNAT classification as Stage 2 or Stage 3. The groups were compared in respect of anthropometric characteristics, APGAR scores, and biochemical parameters. The cases were also separated into 3 groups according to the Troponin-T levels and were compared with respect to the clinical course. The serum Troponin-T (p=0.012), alanine aminotransferase (ALT) and aspartate aminotransferase (AST) (p<0.0001), and lactate levels (p=0.04) in the Sarnat Stage 3 group were statistically significantly higher than in the Sarnat stage 2 group. A significant positive correlation was determined between the Troponin-T level and the total duration of respiratory support (r=0.20, p=0.03). A significant positive correlation was determined between the ALT/AST ratio and the length of stay in hospital (r=0.29, p=0.001), duration of intubation (r=0.32, p=0.01), and total duration of respiratory support (r=0.36, p<0.001). A statistically significant difference was determined in mortality rates between the 3 subgroups of Troponin-T levels; Group 1: 2.8%, Group 2:5.4%, and Group 3: 15.8%. (p=0.04, χ²=4.74). A cut-off value of 164 ng/L for Troponin-T was determined to predict mortality with 77% sensitivity and 67% specificity (AUC=0.73, p=0.023). When the groups were compared according to Troponin-T level, a statistically significant difference was determined in respect of length of stay in hospital (p=0.03, χ²=6.95) and total duration of oxygen support (p=0.01, χ²=9.12). The serum Troponin-T level can be evaluated as a prognostic marker in cases followed up with a diagnosis of NE and receiving hypothermia treatment. There is a need for further prospective studies with larger samples on this subject.