Background/Objectives: Multi-organ failure (MOF) often complicates advanced heart failure (HF), contributing to a poor prognosis. The Model of End-Stage Liver Disease 3.0 (MELD-3.0) scale incorporates liver and kidney function parameters. This study aims to evaluate the prognostic significance of the MELD-3.0 score in patients with advanced HF who have undergone heart transplantation (HTx). Methods: The MELD-3.0 score was computed using the average values of the international normalized ratio and bilirubin, creatinine, sodium, and albumin levels during a hospital stay following HTx. The average MELD-3.0 scores from the period of 1 month preceding HTx and 1 week after HTx were analyzed. The primary endpoint of the study was the 6-month total mortality, and the secondary endpoint was ICU hospitalization time after HTx. Results: The analysis included 106 patients undergoing HTx, with a median age of 53 years (44–63), 81% of whom were male. Within 6 months post-HTx, 17 patients (16%) died; those patients had a higher 1-week post-HTx MELD-3.0 score of 18.3 (14.5–22.7) in comparison to survivors, whose average score was 13.9 (9.5–16.4), p < 0.01. There was no difference in MELD 3.0 score in the pre-HTx period: 16.6 (11.4–17.8) vs. 12.3 (8.6–17.1), p = 0.36. The post-HTx MELD-3.0 score independently predicted death: RR 1.17 (95% CI 1.05–1.30), p < 0.01. A Receiver Operating Characteristic (ROC) determined the cut-off value of the MELD-3.0 score as 17.3 (AUC = 0.83; sensitivity—67%; specificity—86%). Survivors with scores above this value had a longer ICU hospitalization time: 7 (5.0–11.0) vs. 12 (8–20) days (p = 0.01). Conclusions: The post-HTx MELD-3.0 score serves as an independent predictor of an unfavorable prognosis in patients with advanced HF undergoing HTx. The evaluation of MELD-3.0 scores provides additional prognostic information in this population.