In the present study, a robust MHD code “Anupravaha” is utilized to investigate the behavior of magnetohydrodynamic flow within a disaligned channel in the presence of a transverse magnetic field. The performance of the code was rigorously validated considering the benchmark cases such as Hunt and Shercliff’s cases. The study has been carried out considering Hartmann number (Ha) ranges from 10 to 100 and Reynolds number (Re) ranges from 100 to 500. The results of the study show that the disaligned channel creates a distinct flow pattern due to the generation of the Lorentz forces. A large-scale electric circuit is formed near the corners of the disaligned part of the channel, making a region for high volumetric heating. The flow pattern in the disaligned segment is also presented in detail. The study reveals that when the Hartmann number increases from 10 to 100, it shows a sudden drop in the velocity of the fluid flow in the disaligned section due to the MHD effect. This reduces the circulation of flow streamlines, making them more stable and parallel, resulting in less turbulence.