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Using the charmonium light-front wavefunctions obtained by diagonalizing an effective Hamiltonian with the one-gluon exchange interaction and a confining potential inspired by light-front holography in the basis light-front quantization formalism, we compute production of charmonium states in diffractive deep inelastic scattering and ultra-peripheral heavy ion collisions within the dipole picture. Our method allows us to predict yields of all vector charmonium states below the open flavor thresholds in high-energy deep inelastic scattering, proton–nucleus and ultra-peripheral heavy ion collisions, without introducing any new parameters in the light-front wavefunctions. The obtained charmonium cross section is in reasonable agreement with experimental data at HERA, RHIC and LHC. We observe that the cross-section ratio σΨ(2s)/σJ/Ψ reveals significant independence of model parameters.