Pile-Supported Wharves (PSW) are critical for maritime operations but are highly vulnerable to seismic events, which can disrupt port activities. Previous seismic events have highlighted that short free length piles in wharf structures are particularly prone to earthquake damage. This paper aims to mitigate damage between the wharf deck and piles connections by adopting the seismic isolation systems. Conventional Wharf (CW) and Isolated Wharf (IW) structures were comprehensively assessed, focusing on Pile-Soil Interaction (PSI), using the finite element software OpenSees for advanced numerical simulations. Non-Linear Time History Analysis (NLTHA) of CW and IW has been conducted to verify the design under Contingency Level Earthquake (CLE) and Maximum Considered Earthquake (MCE) scenarios. The analysis aims to enhance the performance of short free length piles within the IW structure. Comparative analysis of fragility curves between CW and IW structures shows that isolation systems significantly reduce seismic fragility by 49%, 60%, and 67% at the MCE level for minimal damage, control & repairable damage and life safety protection across three performance levels, respectively. These findings indicate that the implementation of isolation measures has significantly enhanced the seismic performance and safety of PSW structures.