The purpose of the study was to compare the ability of dual energy CT (DECT) and perfusion scintigraphy (PS) to detect pulmonary embolism (PE) in a rabbit model. Gelfoam (n = 20) or saline (n = 4) was injected into the femoral vein of rabbits. After 2 h, DECT pulmonary angiography (CTPA) was used to create blood flow imaging (BFI) and fusion images. The rabbits then underwent PS. Pathological determination of locations and numbers of lung lobes with PE was recorded. The sensitivity and specificity for BFI, CTPA, fused images and PS were calculated using the pathological results as reference standards. Compared with pathological evaluation, CTPA correctly identified PE in 40 lobes and absence of emboli in 80 lobes, corresponding to a sensitivity and specificity of 100%. BFI and fused images correctly identified PE in 40 lobes and the absence of emboli in 78 lobes, corresponding to a sensitivity and specificity of 100% and 98%, respectively. PS correctly detected 27 lobes with PE and 65 lobes without PE, corresponding to a sensitivity and specificity of 68% and 81%, respectively. BFI, CTPA and fused images derived from a single contrast-enhanced DECT provide a higher diagnostic accuracy of detecting PE than PS in a rabbit model.