Abstract In general, submarines are designed to optimize operation below the water surface because they spend most of their time underwater. On the other hand, the performance in the free surface condition is also important because submarines face a variety of scenarios to complete operational missions, and the free surface condition is unavoidable for port departure and arrival. In the case of a submarine, the numerical accuracy of the potential theory for seakeeping analysis is excellent in submerged conditions, but it is poor in free surface conditions because of nonlinear effects near the free surface area. In this study, star-ccm+ was used as a Reynolds-averaged Navier–Stokes (RANS) solver to estimate the seakeeping performance of a Canadian Victoria Class submarine in irregular waves. The results were compared with those of model tests from a published paper. In addition, the potential theory code was also used to assess the seakeeping performance and compare it with computational fluid dynamics (CFD) results. From the calculation results, the motion responses in irregular waves using CFD showed similar trends to the experimental results. In contrast, motion responses from potential code showed significantly larger values than the experimental results. In conclusion, CFD simulations with irregular waves can be a good solution to predict the seakeeping performance of submarines in free surface conditions.