The number of computed tomography (CT) systems in operation in Japan is approximately 4.3 times higher than that of the OECD average. However, CT systems are expensive, and thus, a heavy financial burden for hospital management. We calculate the annual net profits from CT introduction in Japan for single-slice CT (SSCT), multi-slice CT (MSCT), number of hospital beds, and prefecture. We also analyze the factors that affect CT profitability. First, the annual income per CT in operation is estimated for 2011. Second, the annual costs per CT are calculated as the sum of depreciation, maintenance, and labor costs. Finally, the annual net profits per CT are estimated for SSCT and MSCT, the number of hospital beds, and prefecture. A correlation analysis between the annual net profits, population, and number of physicians per CT equipment is used to determine the determinants of the net CT profits by prefecture. Our results show that, for hospitals with fewer than 100 beds, the annual net CT profits are higher for SSCT than MSCT, and vice versa for hospitals with at least 100 beds. Both SSCT and MSCT increased profits as the number of hospital beds increased. The annual net CT profits per prefecture are USD −12,105 for SSCT and USD 87,233 for MSCT, on average. The annual net profits per prefecture and population per CT show positive correlations with both SSCT and MSCT, as do the annual net profits per prefecture and number of physicians per CT. Thus, choosing high-performance MSCT is advantageous in terms of profitability in facilities with at least 100 beds. Additionally, CT profitability presumably affects the balance between the number of introduced CTs, population per CT, and number of physicians per CT.