The purpose of this study was to evaluate the feasibility of gadolinium-enhanced dual energy CT pulmonary angiography (CTPA) to detect pulmonary embolism (PE) in rabbits. Dual energy CT was performed on phantoms composed of different dilution of gadolinium and iodinated contrast agents, CT numbers of the phantoms were measured at different tube voltages. Ten rabbits, which were subdivided into two groups receiving 3 or 5 ml/kg of gadolinium based contrast agent (n = 5 for each group), underwent baseline gadolinium-enhanced dual energy CTPA. The CT numbers of pulmonary arteries were measured. The following day, sponge gelatin was injected into femoral vein of 6 rabbits to create pulmonary emboli. The rabbit were re-imaged 2 h after sponge gelatin injection. Histopathology analysis of the lung lobes was performed. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated. Serum creatinine levels were measured on day 1 before gadolinium contrast media injection, and on day 2 prior to PE creation. The phantoms and animal study showed that the CT numbers of gadolinium-based contrast agent and pulmonary arteries at 80 kVp were higher than those at 140 kVp and average weighted 120 kVp. In 6 rabbits, CTPA showed bilateral pulmonary artery emboli, and the reconstructed gadolinium maps showed decreased pulmonary perfusion in the corresponding lung lobes. With the histopathology results as the reference standards, CTPA and Blood flow imaging (BFI) detected PE in 14 and 14 of the 14 pulmonary lobes, 26, 24 lobes without PE, respectively, corresponding to sensitivities of 100 and 100%, and specificities of 100 and 92%, respectively. Serum creatinine level increased by 6.7 and 20.6% in the rabbits receiving 3 and 5 ml/kg gadolinium based contrast medium respectively. Histopathological analysis found no significant tubular necrosis at either gadolinium dose. Gadolinium-enhanced dual energy CT pulmonary angiography is feasible and it can simultaneously provide information on pulmonary artery and lung perfusion in a rabbit model of PE.