This paper investigates numerically the time dependent hydrothermal behavior of a ferrofluid (water and 4 vol. % Fe3O4) flowing in a helical channel, which is exposed to a nonuniform transverse magnetic field and its walls are subjected to uniform heat flux. The two phase mixture model and control volume technique have been used to study the flow. The results show that applying the nonuniform transverse magnetic field considerably increases the velocity and flow rate in the vicinity of the channel walls while it significantly decreases the velocity at the center of the channel. Applying magnetic field also decreases considerably the temperature of the inner wall of the helical channel. Furthermore, the average Nusselt number is increased by applying the nonuniform transverse magnetic field and it is more enhanced by increasing the magnetic field intensity.