A semi-classical method that incorporates the quantum effects of the low-lying vibrational modes is applied to fusion reactions. The quantum effect is simulated by stochastic sampling of initial zero-point fluctuations of the surface modes. In this model, dissipation of the relative energy into non-collective excitations of nuclei can be included straightforwardly. The inclusion of dissipation is shown to increase the agreement with the fusion cross section data of Ni isotopes.