We derive a holographic prediction of the deconfinement temperature at vanishing chemical potential within a simplest AdS/QCD model with dynamical dilaton. Our analysis leads to a linear relation between and the gluon condensate. After normalizing this relation to the lattice data for pure gauge theory, the standard phenomenological value of gluon condensate from QCD sum rules leads to the prediction MeV which is in a perfect agreement with the modern lattice results and freeze-out temperature measured by the ALICE Collaboration.