Our aim in this study was to perform a cost-effectiveness analysis (CEA) to compare myocardial perfusion magnetic resonance imaging (p-MRI) and single photon emission computed tomography (SPECT) in the Japanese setting. The CEA of p-MRI and SPECT was performed from the payer's perspective. The subjects were outpatients who had chest pain, had no history of myocardial infarction, and showed normal or equivocal stress electrocardiogram findings. The costs of imaging techniques and treatments were assessed with the use of reimbursements of medical fees from Japanese healthcare insurance for the year 2007. Clinical effectiveness was defined in terms of the percent correct diagnosis of coronary artery disease (CAD). Data from published studies provided probabilities for the CEA, including the sensitivity and specificity of each imaging modality. We evaluated the cost-effectiveness ratio (CER) of p-MRI and SPECT using a decision tree model and compared the two. The CERs for diagnosis of CAD by p-MRI and SPECT were 1,988.2 and 2,582.0 Japanese Yen (JPY), respectively. The CERs for diagnosis and treatment of CAD by p-MRI and SPECT were 7,066.1 and 7,172.2 JPY, respectively. At a pre-test likelihood of CAD of 20-70 %, the CERs for diagnosis of CAD by p-MRI and SPECT were 1,476.8-3,364.3 and 2,107.3-3,957.7 JPY, respectively. For outpatients with chest pain, p-MRI had good clinical effectiveness and cost-effectiveness compared with SPECT. In the management of patients with suspected CAD, p-MRI is as useful as SPECT.