The objective of the present study is the active flow control of blood in the aorta with atherosclerosis using an External Magnetic Field (EMF) in order to facilitate the blood flow. For that purpose, a numerical investigation has been developed with a Magneto-hydrodynamics flow modelisation. The blood is considered homogeneous, incompressible and Newtonian and the fluid flow is assumed to be unsteady, two-dimensional and laminar. The aorta tissue is electrically conductive. Fluent software has been used to solve the governing equations. The results relating to velocity, pressure and the wall shear stress indicate that the presence of the EMF considerably influences the blood flow. The flow control deals with the effects of the EMF direction of application and its intensity. The results show that by applying an EMF, the blood velocity and pressure in the aorta are entirely affected. The direction and the intensity of the EMF allow minimization of the flow instabilities due to the geometrical singularities. Therefore, applying an EMF can be considered an appropriate method for flow control in order to obtain a uniform blood circulation around the atherosclerosis.