The selective hydrogenation of pyridines containing reducible groups such as 2‐phenylpyridine typically has low yields due to strong nitrogen coordination with the metal as well as non‐selective 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, maintaining its performance across 8 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 d‐electron deficient Pd trimer.