This retrospective single-centre study compared photon-counting CT (PCCT) with ventilation/perfusion single-photon emission CT (V/Q-SPECT) for quantitative assessment of lobar lung perfusion in patients with suspected or confirmed chronic thromboembolic pulmonary hypertension (CTEPH). The study included 23 patients (mean age: 67.9 ± 10.7 years) who underwent both PCCT and V/Q-SPECT within a median interval of 3 days. Lung perfusion was analysed at both whole-lung and lobar levels using PCCT-derived perfused blood volume maps and V/Q-SPECT perfusion images. Whole-lung perfusion measurements demonstrated a strong correlation between the two techniques (r = 0.72, p < 0.05), while lobar correlations ranged from moderate to strong (r = 0.62–0.85). PCCT yielded slightly higher mean perfusion values compared with V/Q-SPECT, with Bland–Altman analysis showing only a small positive bias (+0.015). Perfusion defect volumes also showed moderate agreement, with a whole-lung correlation of r = 0.60 and lobar correlations ranging from r = 0.49 to 0.77. Overall, these findings support the potential role of PCCT as a reliable imaging approach for simultaneous functional and anatomical lung evaluation in patients with CTEPH. PCCT-based perfusion imaging may therefore represent a feasible single-modality alternative to the conventional multimodal techniques.