Protecting low coordinated sites (LCS) of Pt nanoparticles, which are vulnerable to dissolution, may be an ideal solution for enhancing the durability of polymer electrolyte fuel cells (PEMFCs). However, the selective protection of LCSs without deactivating the other sites presents a key challenge. Herein, we report the preferential protection of LCSs with a thiol derivative having a silane functional group, (3-mercaptopropyl) triethoxysilane (MPTES). MPTES preferentially adsorbs on the LCSs and is converted to a silica framework, providing robust masking of the LCSs. With the preferential protection, the initial oxygen reduction reaction (ORR) activity is marginally reduced by 8% in spite of the initial electrochemical surface area (ECSA) loss of 30%. The protected Pt/C catalyst shows an ECSA loss of 5.6% and an ORR half-wave potential loss of 5 mV after 30,000 voltage cycles between 0.6 and 1.0 V, corresponding to a 6.7- and 2.6-fold durability improvement compared to unprotected Pt/C, respectively. The preferential protection of the vulnerable LCSs provides a practical solution for PEMFC stability due to its simplicity and high efficacy.