We investigate computationally the transport characteristics for flow of MWCNT-Fe3O4/H2O hybrid nanofluid through a wavy channel under the influence of an externally applied magnetic field. The flow and temperature fields are analyzed in terms of streamlines, isotherms, average Nusselt number ((Formula presented.)), magnetic enhancement ratio (ERm), and magnetic performance factor (PFm) for the following range of parameters: 100 (Formula presented.) Re (Formula presented.) 500, 0 (Formula presented.) Ha (Formula presented.) 10, and 0% (Formula presented.) 0.3%. The strength of the reverse flow in the recirculatory zones decreases with Ha, and beyond a critical Ha, the flow becomes attached even in the diverging part of the channel. The hot spot intensity near the walls decreases and hence, the value of (Formula presented.) increases with the increase in volume fraction of nano-particles and Ha. The rate of increment of (Formula presented.) is steeper at lower values of Ha. It further reveals that PFm monotonically decreases with Ha for lower Re (= 100). For higher values of Re, PFm decreases with Ha for its lower and higher values, while for the intermediate range of Ha, PFm increases with Ha.