The elements that possess the ability of changing the flow structure (neckings, nozzles, valves, elbows) can be found in numerous industrial and medical applications. This ability leads to the velocity and temperature fields modification and can be a reason of negative effects like pressure loss. These negative effects can be reduced by the usage of magnetic field. Magnetic control of weakly magnetic fluids' velocity and temperature distributions is well known. Presented paper considers the numerical analysis of velocity and temperature maldistribution due to the influence of strong magnetic field. The analysis was carried out for threedimensional circular duct with simplified stenosis (narrowing of the blood vessels), which took form of confusor-diffuser section of the pipe. The system included duct and the magnetic coil that was oriented perpendicularly to the flow axis and placed in between confusor and diffuser. The wall of the stenosis was divided into subzones partially heated in order to control the velocity and temperature fields. Biot-Savart's law was applied to calculate the distribution of the magnetic field, which was then used to obtain the magnetic force distribution and added to principle of conservation of momentum equations as the external body force. Commercially available software Ansys Fluent 13 was chosen to conduct the numerical analysis, however special user-defined modulus to calculate the distribution of magnetic force was prepared and implemented in it. The results pointed out that the usage of magnetic field might provide a significant change in both velocity and temperature distribution, especially for low Reynolds number flows.