Abstract In this paper, we investigate the impact of an inclined magnetic field of uniform intensity on viscous, incompressible pressure-driven Stokes flow through a slip-patterned, rectangular microchannel using the boundary element method based on the stream function-vorticity variables approach. The present investigation focuses only on the out-phase slip patterning of the microchannel walls. We address two scenarios of slip patterning, specifically large and fine slip patterning, which are determined by the periodicity of the patterning. We utilized the no-slip and Navier’s slip boundary conditions in an alternative manner on the walls. The Stokes equations govern the viscous flow through a microchannel. We assume a very small magnetic Reynold’s number to eliminate the equation of induced magnetic field in the present study. We analyzed the impact of considered dimensionless hydrodynamic parameters, including the Hartman number (Ha), inclination angle (θ) of the magnetic field, and the slip length (ls ) on fluid dynamics. In the case of fine slip, we observed significant variations in both velocity and pressure gradient, in contrast to large slip patterning. Fine slip patterning significantly increases the shear stress at slip regimes, while large slip periodicity significantly reduces it at no-slip regimes. The present investigation has several notable implications, such as regulation and advancement of mixing and heat transmission within microfluidic systems.