Early diagnosis of coronary artery disease is very vital for success in treatment of this disease. However, the appropriate diagnostic modality for diagnosis of coronary artery disease is uncertain. Therefore, we conducted this study to compare the cost-effectiveness of Single-Photon Emission-Computed Tomography (SPECT) versus stress echocardiography for diagnosis of coronary artery disease in Iran. A decision tree model was developed to compare the cost-effectiveness of SPECT versus stress echocardiography. This study was conducted in Tehran, capital of Iran, between April 1, 2017, and September 1, 2018. The cost analysis was conducted from a societal perspective and medical direct costs, nonmedical direct costs and indirect costs were estimated. Effectiveness was defined as the accurate detection of coronary artery disease and invasive coronary angiography was used as a gold standard. The incremental cost-effectiveness ratio was defined as an additional cost per correct diagnosis. SPECT was associated with higher costs and lower effectiveness compared with stress echocardiography. Therefore, stress echocardiography is dominant alternative compared to SPECT. The results also indicated that total cost per patient were $970.49 and $781.8 for SPECT and stress echocardiography, respectively. Also, the percent of true positive and true negative responses were %88 and %79 for SPECT and %90 and %92 for stress echocardiography. The results of this study indicate that stress echocardiography is the cost-effective modality in the diagnosis of coronary artery disease compared with SPECT. According to the results, it is suggested cardiologists use stress echocardiography instead of SPECT for the diagnosis of coronary artery disease. The result of the current study has significant concepts for decision-making in designing clinical guidelines for the diagnosis of coronary artery disease.