Convective ferrofluid heat transfer in a microchannel under static (SMF) and rotating magnetic fields (RMF) has been investigated. The microchannel has a cylindrical pit in which a heat source with a constant heat flux is applied on the bottom wall. The top wall of pit is positioned next to a rotational permanent magnet that creates RMF, while it is stationary for SMF. The heat transfer characteristic results at various flow rates, magnetic field inductions (B) and nanoparticle volume fractions (phi = 0.1-2%) by applying RMF have been compared to those of SMF. Results depicted that using ferrofluid results in improvement of heat transfer rate compared to DI-water. However, applying SMF causes to reduction in the heat transfer characteristic. Results illustrated that RMF is more effective compared to SMF. In RMF, the influence of B and rotational speed of magnet (W) have been considered; heat transfer characteristics enhanced by increasing B and W. The effect of W more than 18 rad/s is not significant. The effect of increase in phi on heat transfer coefficient is also evaluated and increasing trend is observed. Maximum value of heat transfer coefficient is achieved for RMF with B = 1100 mT, W = 18 rad/s and MNPs concentration of 2%.