Objectives To evaluate the concordance between DECT perfusion and ventilation/perfusion (V/Q) scintigraphy in diagnosing chronic thromboembolic pulmonary hypertension (CTEPH). Methods Eighty patients underwent V/Q scintigraphy and DECT perfusion on a 2nd- and 3rd-generation dual-source CT system. The imaging criteria for diagnosing CTEPH relied on at least one segmental triangular perfusion defect on DECT perfusion studies and V/Q mismatch on scintigraphy examinations. Results Based on multidisciplinary expert decisions that did not include DECT perfusion, 36 patients were diagnosed with CTEPH and 44 patients with other aetiologies of PH. On DECT perfusion studies, there were 35 true positives, 6 false positives and 1 false negative (sensitivity 0.97, specificity 0.86, PPV 0.85, NPV 0.97). On V/Q scans, there were 35 true positives and 1 false negative (sensitivity 0.97, specificity 1, PPV 1, NPV 0.98). There was excellent agreement between CT perfusion and scintigraphy in diagnosing CTEPH (kappa value 0.80). Combined information from DECT perfusion and CT angiographic images enabled correct reclassification of the 6 false positives and the unique false negative case of DECT perfusion. Conclusion There is excellent agreement between DECT perfusion and V/Q scintigraphy in diagnosing CTEPH. The diagnostic accuracy of DECT perfusion is reinforced by the morpho-functional analysis of data sets. Key Points • Chronic thromboembolic pulmonary hypertension (CTEPH) is potentially curable by surgery. • The triage of patients with pulmonary hypertension currently relies on scintigraphy. • Dual-energy CT (DECT) can provide standard diagnostic information and lung perfusion from a single acquisition. • There is excellent agreement between DECT perfusion and scintigraphy in separating CTEPH and non-CTEPH patients.