Pulmonary hypertension (PH) risk assessment tools are widely used to evaluate prognosis and guide treatment decisions, particularly for timing of lung transplantation. However, their applicability to patients with chronic thromboembolic pulmonary hypertension (CTEPH) undergoing pulmonary thrombo-endarterectomy (PTE) has not been fully assessed. This study retrospectively applied three validated PH risk scores—COMPERA, REVEAL 2.0, and the 4-Strata model—to preoperative data from 506 patients who underwent PTE between 2005 and 2023. Patients were stratified into low, intermediate, and high-risk categories based on each score. Postoperative outcomes and long-term survival were compared across risk groups and between scoring systems. Analysis revealed that higher preoperative risk scores were associated with more complex postoperative courses, including longer mechanical ventilation, ICU stay, and hospital length of stay, as well as increased 90-day mortality and ECMO use. The 4-Strata model demonstrated superior stratification, with clearer distinctions in outcomes between risk levels. Multivariate analysis identified age and high-risk status in the 4-Strata model as independent predictors of 90-day mortality. Long-term survival analysis confirmed that higher risk scores correlated with poorer outcomes across all models, with the 4-Strata score offering the best discrimination. These results support the use of PH-specific risk scores in the surgical management of CTEPH and highlight the potential of the 4-Strata model as a prognostic tool. The study underscores the importance of integrating risk stratification into shared clinical decision-making.