This paper presents a numerical analysis of blood flow in a diseased vessel within the presence of an external magnetic field. The blood flow was considered to be incompressible and fully developed, in that the non-Newtonian nature of the fluid was characterised as a generalised power law model for shear-thinning, Newtonian, and shear-thickening fluids. The impact of a transverse directed external magnetic field on blood flow through a stenosed bifurcated artery was investigated. The arterial geometry was considered as a bifurcated channel with overlapping shaped stenosis. The problem was treated mathematically using the Galerkin Least-Squares (GLS) method. The implementation of this numerical method managed to overcome the numerical instability faced by the classical Galerkin technique when adopted to a highly viscous flow. The benefit of GLS in circumventing the Ladyzhenskaya-Babuška-Brezzi (LBB) condition was utilized by evaluating both the velocity and pressure components at corner nodes of a unstructured triangular element. The non-linearity that emerged from the convective terms was then treated using the Newton-Raphson method, while the numerical integrals were computed using a Gaussian quadrature rule with six quadrature points. The findings obtained from this study were then compared with available results from the literature as well as Comsol multiphysics software to verify the accuracy and validity of the numerical algorithms. It was found that the application of magnetic field was able to overcome flow reversal by 39% for a shear-thinning fluid, 26% for a Newtonian fluid, and 27% for a shear-thickening fluid. The negative pressure and steep wall shear stress which occurs at the extremities of an overlapping stenosis throat were diminished by rise in magnetic intensity. This prevented thrombosis occurrence and produced a uniform calm flow.