This paper describes a possibility of heat transfer enhancement in a mm-scale flow channel by using a combination of some projections and pulsating flow. The objective of this research is to develop a novel heat exchanger for miniaturized productions such as high-density packaging electronic equipment by applying pulsating flow to enhance heat transfer while inhibiting an increase of pressure drop. In order to evaluate the possibility of applying pulsating flow to miniature water channels, a three-dimensional flow and heat transfer analysis was performed. Heat transfer performance of a combination of pulsating water flow and a projection was investigated. The mechanism of heat transfer enhancement by the proposed combination was also investigated. The proposed combination enhances heat transfer in the channel remarkably. Heat transfer performance of pulsating flow around the projection was approximately 80% higher than that of steady flow in the channel without the projection. This was caused by the generation of counter flow behind the projection during the deceleration period. The counter flow ejected heated water near the projection and heat transfer enhancement is achieved.