We investigate the superfluid dynamics of a Josephson junction beyond the mean-field description, incorporating the role of thermal fluctuations as well as quantum fluctuations. Using a formalism that accounts for the fluctuations in a homogeneous gas, and under the assumption that the transport of the non-condensed component is negligible, we derive a modified equation of motion within the two-site approximation. The resulting corrections for the typical dynamical quantities, like the Josephson frequency, the strength of macroscopic quantum self-trapping, and the threshold for spontaneous symmetry breaking, allow us to predict the effects of both types of fluctuations and assess their relative importance in different regimes in a semianalytical fashion. For all the dynamical quantities, the quantum fluctuations are shown to play an opposite role with respect to the thermal fluctuations. Josephson frequency is decreased by thermal fluctuations and both the critical strenghts of macroscopic quantum self trapping and spontaneous symmetry breaking are increased. We assess the experimentally accessible regimes by calculating the relevant parameters of recent experimental realizations of Bosonic Josephson junction and show that the expected regime is dominated by quantum fluctuations.