The selective hydrogenation of pyridines containing reducible groups such as 2-phenylpyridine (PPY) typically has low yields due to strong nitrogen coordination with the metal as well as nonselective and over-hydrogenation. We report the synthesis of a novel Pd trimer catalyst through confined growth on an ordered mesoporous carrier, characterized by a 0.42 d-electron deficiency to address this challenge. This catalyst achieved a nearly complete conversion of 2-phenylpyridine and selectivity to 2-phenylpiperidine (PPD), maintaining its performance across eight batch cycles and continuous flow in the liquid phase for 800 h with negligible loss of activity or selectivity. We discuss the roles of active sites, including Pd d charge and ensemble structure, in relation to activation entropy, a Hammett study, and the adsorption configuration of the reactant. The exceptional 2-phenylpyridine hydrogenation activity and selectivity are attributed to the adsorption constraint of the pyridyl ring and the stabilization of the negatively charged transition state in the rate-determining step produced by the d-electron deficient Pd trimer.