At present great attention is given to a problem of research of hydrodynamics and heat exchange in pulsating flows. Experimental studies for the flow in smooth channels show that pulsation of fluid flow significantly affects heat transferring and can be accompanied by both reduction and increasing in the intensity of heat exchange. However, at the present day, there is little reliable information about the effect of a pulsating flow on heat transferring in channels with discrete roughness. Thus, detection of regularities in heat exchanging processes of such flows in discretely rough channels is an actual problem for today. In this paper the results of numerical simulation of heat exchange in smooth and discrete-rough channels with a pulsating motion of fluid in them are presented. It is revealed that in the pulsating flow the instantaneous values of the heat exchange coefficient change with the change in the instantaneous values of the Reynolds numbers. Three zones of influence of the pulsing flow on the heat exchange in the channels are established. In the first area, with the Strouhal numbers 0 < Sh < 2, increasing in the average value of heat exchange in 10-15 % is observed. In the second area 2 < Sh < 4.3, its decreasing in 10-15 %. In the third area, 4.3 < Sh < 6, the average value of the heat exchanging value becomes almost the same as for the case of a stationary flow.