Atomic lattice clocks have spurred numerous ideas for tests of fundamental physics, detection of general relativistic effects, and studies of interacting many-body systems. On the other hand, molecular structure and dynamics offer rich energy scales that are at the heart of new protocols in precision measurement and quantum information science. Here we demonstrate a fundamentally distinct type of lattice clock that is based on vibrations in diatomic molecules, and present coherent Rabi oscillations between weakly and deeply bound molecules that persist for 10s of milliseconds. This control is made possible by a state-insensitive magic lattice trap that weakly couples to molecular vibronic resonances and enhances the coherence time between molecules and light by several orders of magnitude. The achieved quality factor $Q=8times10^{11}$ results from 30-Hz narrow resonances for a 25-THz clock transition in Sr$_2$. Our technique of extended coherent manipulation is applicable to long-term storage of quantum information in qubits based on ultracold polar molecules, while the vibrational clock enables precise probes of interatomic forces, tests of Newtonian gravitation at ultrashort range, and model-independent searches for electron-to-proton mass ratio variations.
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