A new uncertainty quantifier is presented for linear transfer functions of wave-induced ship motions and loads obtained by various seakeeping codes. The numerical simulations are conducted for the high-speed Flokstra container ship in regular waves at various heading angles, and the results are compared with existing experimental data. The study employs five numerical codes that are based on three different seakeeping theories, namely strip theory, 3D frequency-domain method, and 3D time-domain method. Multiple measures are applied to quantify the uncertainty in the calculated transfer functions, such as frequency-independent model error, coefficient of determination, and the total difference. In addition, a new measure of uncertainty, termed modified total difference, is proposed for determining the uncertainty of individual seakeeping codes based on experimental data rather than the mean of results obtained by numerical codes. Results show that the uncertainty measures can identify differences between the codes. The predicted wave-induced loads have higher uncertainties compared to motions. The uncertainty assessment shows that none of the applied codes can produce accurate estimates for all wave-induced motions and loads at all heading angles at the same time.