A self-consistent mean field theory is introduced and used to investigate the thermodynamics and spin dynamics of an S = 1 quantum spin system with a magnetic Skyrmion. The temperature dependence of the Skyrmion profile as well as the phase diagram are calculated. In addition, the spin dynamics of a magnetic Skyrmion is described by solving the time dependent Schrdinger equation with additional damping term. The Skyrmion annihilation process driven by an electric field is used to compare the trajectories of the quantum mechanical simulation with a semi-classical description for the spin expectation values using a differential equation similar to the classical Landau-Lifshitz-Gilbert equation.