This retrospective study was performed to systemically compare several candidates for optimal contrast enhancement protocols of cardiothoracic CT dedicated for evaluating the Fontan pathway. Of 115 CT examinations from 89 patients, simultaneous injection of contrast agent via the arm and leg veins with 50% diluted contrast agent (group 1, n = 38), 60-second scan delay after leg vein injection (group 2, n = 41) or 3-minute scan delay (group 3, n = 36) was used to obtain optimal contrast enhancement. The degree and heterogeneity of cardiovascular enhancement, image noise, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) were quantitatively evaluated. Histogram-assisted semi-quantitative evaluation was performed for heterogeneous enhancement, and a cut-off value indicating heterogeneous enhancement was determined by comparing the standard deviations between the cases showing homogeneous and heterogeneous enhancement. Contrast enhancement of the Fontan pathway, the standard deviation measured in the Fontan pathway, SNR, and CNR were more frequently lower in group 3 compared to groups 1 and 2 (p < 0.001). Homogeneous enhancement of the Fontan pathway based on the histogram-assisted semi-quantitative evaluation was more frequently seen in group 3 compared to groups 1 and 2 (p < 0.043‒0.001). Receiver operating characteristic curve analysis demonstrated that the standard deviation was an excellent diagnostic test in determining the homogeneity of contrast enhancement (area under the curve = 0.991; 95% confidence interval, 0.988‒0.994; p < 0.001). Standard deviations > 105.1 HU could be considered to indicate heterogeneous enhancement with 73.2% sensitivity and 100.0% specificity. The protocol using a 3-minute scan delay best achieved homogeneous contrast enhancement in the Fontan pathway on cardiothoracic CT among the tested protocols. However, low contrast enhancement, SNR, and, CNR need to be improved.