Chronic thromboembolic pulmonary hypertension (CTEPH) is an ominous disease leading to progressive right ventricular failure (RVF) and death. There is no reliable risk stratification strategy for patients with CTEPH. The pulmonary artery pulsatility index (PAPI) is a novel hemodynamic index that predicts the occurrence RVF. We aimed to investigate prognostic value of PAPI in inoperable CTEPH. Consecutive patients with inoperable CTEPH were enrolled. PAPI was calculated from baseline right heart catheterization data. A prognostic cut-off value was determined, and characteristics of low- and high-PAPI groups were compared. The association between risk assessment and survival was also evaluated. We included 50 patients (mean age 64 ± 12.2 years, 60% female). The number of deaths was 12 (24%), and the mean follow-up time was 52 ± 19.3 months. The established prognostic cut-off value for PAPI was 3.9. The low-PAPI group had significantly higher mean values of mean atrial pressure (14.9 vs. 7.8, p = 0.0001), end-diastolic right ventricular pressure (16.5 vs. 11.2, p = 0.004), and diastolic pulmonary artery pressure (35.8 vs. 27.7, p = 0.0012). The low-PAPI group had lower survival as compared to high-PAPI (log-rank p < 0.0001). PAPI was independently associated with survival and may be applicable for risk stratification in inoperable CTEPH.