Using two-dimensional numerical simulations of the momentum, mass, and energy conservation equations, we investigate the enhancement of heat transfer in a rectangular micro-fluidic channel. The fluid inside the channel is assumed to be stationary initially and actuated by the motion imparted by mechanical stirrers, which are attached to the bottom of the channel. Based on the direction of the oscillation of the stirrers, the boundary conditions can be classified as either no-slip (when the oscillation is perpendicular to the length of the channel) or periodic (when the oscillation is along the length of the channel). The heat transfer enhancement due to the motion of the stirrers (with respect to the stationary stirrer situation) is analyzed in terms of the Reynolds number (ranging from 0.7 to 1000) and the Peclet number (ranging from 10 to 100). We find that the heat transfer first increases and then decreases with an increase in the Reynolds number for any given Peclet number. The heat transferred is maximum at a Reynolds number of 20 for the no-slip case and at a Reynolds number of 40 for the periodic case. For a given Peclet and Reynolds number, the heat flux for the periodic case is always larger than the no-slip case. We explain the reason for these trends using time-averaged flow velocity profiles induced by the oscillation of the mechanical stirrers.