This study aimed to address the role of various inflammation-related blood indices for the assessment of in-hospital outcomes in subjects undergoing Glenn procedure. Subjects who underwent the Glenn procedure for hypoplastic left heart syndrome were analysed retrospectively. Subjects were divided into two groups: Group 1 consisted of 78 patients who were discharged, and Group 2 included 12 patients who died after surgery. Post-operative third-day neutrophil count and neutrophil-to-lymphocyte ratio value were significantly higher in the exitus group compared to the discharged group (p = 0.006 and p = 0.003, respectively). Third-day neutrophil-to-lymphocyte ratio was positively correlated with duration of intubation (r = 0.253, p = 0.018), length of stay in ICU (r = 0.296, p = 0.006) and length of hospital stay (r = 0.297, p = 0.005). Multiple logistic regression analysis revealed that patients with high third-day neutrophil-to-lymphocyte ratio (≥6) had 14.227-fold higher risk of death compared to those with lower values. In addition, higher pulmonary arterial pressure was associated with increased risk of death. Receiver operating characteristics analysis revealed that neutrophil-to-lymphocyte ratio had 66.67% sensitivity, 84% specificity, 81.61% accuracy, 40.00% positive predictive value and 94.03% negative predictive value with a cut-off point of ≥6 to predict mortality. Third-day neutrophil-to-lymphocyte ratio and increased post-operative pulmonary arterial pressure are significant predictors for in-hospital mortality in Glenn procedure recipients. A cut-off value of ≥6 for third-day neutrophil-to-lymphocyte ratio predicts mortality with 66.67% sensitivity and 84% specificity. Given its simplicity and availability, post-operative neutrophil-to-lymphocyte ratio should be monitored on a daily basis to identify patients with high risk for mortality after Glenn procedure.