Pier structures in port and fishing harbor facilities require dynamic analyses during the design phase to account for external dynamic forces because of their high flexibility. Dynamic forces are frequently approximated as equivalent static forces for design purposes in practical engineering applications, but the fluctuational effects induced by these dynamic forces can be neglected. As the frequency range of wave forces acting on pier structures (0.05–1.0 Hz) significantly overlaps with the typical natural frequency range of pier structures (0.25–4.0 Hz), the response of a pier structure can be amplified because of the dynamic effects of the waves. In this study, we conducted a dynamic analysis by applying wave forces—a representative dynamic load—to a pier structure. The results were compared with those from a static analysis. A fatigue life assessment, which is often overlooked in static analyses, was also performed. The findings indicated that the concrete at the connection between the upper pier and steel piles exhibited a fatigue life of 27.3 years. The steel piles exhibited fatigue lives of 27.1 and 8.3 years depending on the weld details, falling short of the expected structural durability. Based on these results, recommendations for pier structures are proposed.