On the basis of the closed-time path formalism of non-equilibrium quantum field theory, we derive the real-time quantum dynamics of heavy quark systems. Even though our primary goal is the description of heavy quarkonia, our method allows a unified description of the propagation of single heavy quarks as well as their bound states. To make calculations tractable, we deploy leading-order perturbation theory and consider the non-relativistic limit. Various dynamical equations, such as the master equation for quantum Brownian motion and time-evolution equation for heavy quark and quarkonium forward correlators, are obtained from a single operator, the renormalized effective Hamiltonian. We are thus able to reproduce previous results of perturbative calculations of the drag force and the complex potential simultaneously. In addition, we present stochastic time-evolution equations for heavy quark and quarkonium wave function, which are equivalent to the dynamical equations.