We present an optimal design of magnetic field for reaction control in drug delivery applications by nonlinear topology optimization method. In this model, the objective is to find the optimal distribution of a magnetic field in a blood artery such that the axial velocity component at the center of the channel is minimized. Our implementation allows a wide range of optimization objectives, such as gene transfer and drug delivery, to be dealt with straightforwardly. Topology optimization of the Navier-Stokes equations is encountered in different branches and applications. We demonstrate our method by studies of steady-state Navier–Stokes flow problems, as well as encompassing the topology optimization of fluids in Stokes flow. We analyze the physical aspects of the solutions and how they are affected by different parameters of the optimization algorithm.