The Fokker-Planck PDE describes the dynamics of several biochemical and biological processes, as well as of phenomena at molecular scale. In this paper, the problem of feedback control of the Fokker-Planck PDE is studied. It is shown that the procedure for numerical solution of Fokker-Planck PDE results into a set of nonlinear ordinary differential equations (ODEs) and an associated state equations model. For the local subsystems, into which a Fokker-Planck PDE is decomposed, it becomes possible to apply boundary-based feedback control. The controller design proceeds by showing that the state-space model of the Fokker-Planck PDE stands for a differentially flat system. Next, for each subsystem which is related to a nonlinear ODE, a virtual control input is computed, that can invert the subsystem's dynamics and can eliminate the subsystem's tracking error. From the last row of the state-space description, the control input (boundary condition) that is actually applied to the Fokker-Planck PDE system is found. This control input contains recursively all virtual control inputs which were computed for the individual ODE subsystems associated with the previous rows of the state-space equation. Thus, by tracing the rows of the state-space model backwards, at each iteration of the control algorithm, one can finally obtain the control input that should be applied to the Fokker-Planck PDE system so as to assure that all its state variables will converge to the desirable setpoints.