The effects of hull-girder vibration on the fatigue strength of a Post-Panamax container ship are discussed in the present paper. Firstly, the short-term sea states are categorized according to the occurrence probability of each sea state. Time histories of hull-girder stress in short-term sea states are calculated by means of a nonlinear simulation code of ship response assuming that the hull-girder is rigid and flexible. Then, the calculated stress peaks are processed by the rainflow counting method, where two different counting procedures are used based on the considerations of crack propagation behaviors. Finally, the fatigue damage in life time of the ship in each categorized short-term sea state is estimated by means of Miner’s rule. Based on the calculated results, the effects of hull-girder vibrations on the fatigue damage are clarified by disaggregated damage from short-term sea state.