In this paper, results of applying a non‐uniform magnetic field on a dilute ferrofluid (water and 3% vol. Fe3O4) flow in a corrugated channel under a constant heat flux boundary condition have been reported. The thermal behavior of the flow is investigated numerically using a two‐phase mixture model and control volume technique. It is concluded that using a magnetic field with a negative gradient on a nanofluid flow in corrugated channels can be proposed as a suitable method to achieve higher heat transfer performance and augment the heat transfer coefficient and also reduces the wall temperature. This method can lead to the design of more compact heat exchangers.