This paper presents the effect of introducing a porous medium on the flow regime and heat transfer of a two-dimensional channel through which the flow is reciprocating. The channel is discretely heated from above and is insulated in the bottom which can simulate a cooling mechanism for compact circuit boards. In this ideal geometry, a fully developed reciprocating flow is established via oscillating pressure gradient. In side boundaries, velocity and temperature are assumed to be periodic. A certain volume of this channel is occupied by a porous medium which is shown to be an effecting tool for augmentation of heat transfer. At first, Momentum equations of the domain are solved analytically (Brinkman-extended Darcy model is used for porous region) and then the energy equation is solved numerically using alternating direction implicit (ADI) method. Finally a case study is investigated for a high-porous and high-conductive medium (Aluminum alloy T-6201) and the enhancing effect and optimization criteria are discussed in the result section.