Confidence levels of the seakeeping experiment results can be assessed through uncertainty analysis. The seakeeping experiments with a free-running model system were carried out in the manoeuvring and ocean engineering basin (MOB) at the Indonesian Hydrodynamic Laboratory (IHL) using uncertainty techniques to improve the experiment quality. The method used is the International Organization for Standardization, Guide for Uncertainty of Measurements (ISO-GUM), type A and B uncertainty, which is the foundation for the uncertainty analysis for seakeeping experiment recommendations released by the International Towing Tank Conference (ITTC). This research aims to determine the combined uncertainty value of the seakeeping experiment on a benchmark ship model with a scale of 1:62, representing the full scale of 186 meters. Seakeeping testing is carried out under head and beam waves, each with regular waves at one wave height (Hs) with three different wave periods (Tw). The experimental seakeeping result, generally, has the same tendency in each heave, pitch, and roll motion mode. The expanded uncertainty with 95% confidence level of the RAO-Heave uncertainty in all period conditions is always less than 3%, RAO-Pitch uncertainty in all period conditions is always less than 1%, and RAO-Roll uncertainty in all period conditions is always less than 1.2%. These uncertainties are quite small.