Magnetic drug targeting can be used for treating stenosis and thrombosis in partly occluded blood vessels. Herein, a numerical investigation of magnetic drug targeting using functionalized magnetic microspheres in partly occluded blood vessels is conducted. An Eulerian-Lagrangian technique is adopted to resolve the hemodynamic flow and the motion of the magnetic particles in the flow. An implantable cylindrical permanent magnet insert is used to create the requisite magnetic field. Targeted transport of the magnetic particles in a partly occluded vessel differs distinctly from the same in a regular unblocked vessel. Parametric investigation is conducted, and the influence of the flow Re, magnetic insert diameter, and its radial and axial position on the “targeting efficiency” is reported. Analysis shows that there exists an optimum regime of operating parameters for which deposition of the drug-carrying magnetic particles in a predesignated target zone on the partly occluded vessel wall can be maximized. The results provide useful design bases for an in vitro setup for the investigation of magnetic drug targeting in stenosed blood vessels.