The E/Z stereocontrol in a C=C bond is a fundamental issue in olefin synthesis. Although the thermodynamically more stable E geometry is readily addressable by thermal Z to E geometric isomerization through equilibrium, it has remained difficult to undergo thermal geometric isomerization to the reverse E to Z direction in a selective manner, because it requires kinetic trapping of Z-isomer with injection of chemical energy. Here we report that a dinuclear PdI-PdI complex mediates selective isomerization of E-1,3-diene to its Z-isomer without photoirradiation, where kinetic trapping is achieved through rational sequences of dinuclear elementary steps. The chemical energy required for the E to Z isomerization can be injected from an organic conjugate reaction through sharing of common Pd species.