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Background: The gamma emission tomography (GET) device has been reported a reliable technique to inspect partial defects within spent nuclear fuel (SNF) of pin-by-pin level. However, the existing GET devices have low accuracy owing to the high attenuation and scatter probability for SNF inspection condition. The purpose of this study is to design and optimize a Yonsei single-photon emission computed tomography version 2 (YSECT.v.2) for fast inspection of SNF in water storage by acquisition of high-quality tomographic images. Materials and Methods: Using Geant4 (Geant4 Collaboration) and DETECT-2000 (Glenn F. Knoll et al.) Monte Carlo simulation, the geometrical structure of the proposed device was determined and its performance was evaluated for the 137Cs source in water. In a Geant4-based assessment, proposed device was compared with the International Atomic Energy Agency (IAEA)-authenticated device for the quality of tomographic images obtained for 12 fuel sources in a 14 × 14 Westinghouse-type fuel assembly. Results and Discussion: According to the results, the length, slit width, and septal width of the collimator were determined to be 65, 2.1, and 1.5 mm, respectively, and the material and length of the trapezoidal-shaped scintillator were determined to be gadolinium aluminum gallium garnet and 45 mm, respectively. Based on the results of performance comparison between the YSECT.v.2 and IAEA’s device, the proposed device showed 200 times higher performance in gamma-detection sensitivity and similar source discrimination probability. Conclusion: In this study, we optimally designed the GET device for improving the SNF inspection accuracy and evaluated its performance. Our results show that the YSECT.v.2 device could be employed for SNF inspection.