The study aims to investigate the effect of uniform inclined magnetic field on two‐dimensional flow of a steady, viscous incompressible fluid at low Reynolds number through a porous wavy channel. We consider a channel having sinusoidal walls filled with a fully saturated porous medium. The porous regime is assumed to be homogenous and isotropic. The viscous flow through a porous regime is governed by Brinkman equation, where the viscous forces are dominant. This allows us to assume the no‐slip boundary conditions at the walls of the wavy channel. Boundary element method (BEM) based on non‐primitive variables namely, stream function‐vorticity variables is used to solve the Brinkman equation. Further, we consider a very small magnetic Reynolds number to eliminate the magnetic‐induced equation. We analyzed that an increase in Hartman number, porosity, and reduction in inclination angle of magnetic field, wave amplitude, and Darcy number led to a reduction in horizontal velocity, whereas an increase in Hartman number, porosity, wave amplitude, and decrease in Darcy number and angle of inclination of magnetic field led to an increase in vertical velocity. Moreover, the flow reversal phenomena occur in the vicinity of the crest regime of the porous wavy channel for high wave amplitude and low Hartman number. The proposed investigation has widespread applications, such as drug delivery systems to target the drug precisely, magneto‐hydrodynamic pumps to regulate the blood flow in artificial hearts to reduce the risk of blood clotting, and so forth.