Background: The primary aim of this study was to evaluate the performance of four burn prognostic scores—Abbreviated Burn Severity Index (ABSI), Ryan, Belgium Outcome Burn Injury (BOBI), and revised Baux score (rBaux) in a Croatian burn center. A secondary aim was to compare patient outcomes before and after the organizational and protocol changes. Methods: A retrospective study and comparison of four prediction scores was conducted over a nine-year period in burn patients with ≥20% total body surface area (TBSA) burned. Additionally, outcomes before and after organizational changes were compared. Results: A total of 149 patients were included, with the mean patient age of 54.62 ± 19.38 years, the mean of TBSA of 42.98 ± 19.90, and an overall mortality rate of 48.99%. The area under the ROC curve (AUROC) was 0.79 for the rBaux and ABSI score, 0.77 for the BOBI score, and 0.76 for the Ryan score. The duration of mechanical ventilation and length of stay (LOS) in burn intensive care units (BICU) decreased after the organizational changes, though survival rates remained similar. Conclusions: Prognostic scores are good predictors of mortality but with moderate predictive accuracy. Continuity of care in intensive care could be important for better outcomes.