PurposeThis paper aims to numerically investigate the thermal performance evaluation of a microchannel with different porous media insert configurations.Design/methodology/approachHeat transfer and pressure drop of fluid flow through a three-dimensional (3D) microchannel with different partially and filled porous media insert configurations are investigated numerically. The number of divisions and positions of porous material inside the microchannel for 12 different arrangements are considered. A control volume method is used for single-phase laminar flow with the Darcy–Forchheimer model used for the porous media. The geometry of the problem consists of a microchannel with a rectangular cross-section of 0.4 mm × 0.2 mm and length 20 mm, with a stainless steel porous material insert with a porosity coefficient of ε = 0.32 and a Darcy number of Da = 2.7 × 10−4.FindingsNumerical results show that when the transverse arrangement is used, as the number of partitions increases, the thermal performance is improved and the heat transfer increases up to 300% compared to that of the plain microchannel. Comparing the obtained results from the microchannels with transverse and longitudinal configurations, at low Reynolds numbers, the transverse arrangement of porous blocks and at high Reynold numbers, the longitudinal arrangement present the best thermal performance which is virtually four times higher compared to the obtained Nu numbers from the plain microchannel. The results show that as the volume of porous material is constant in the cases with various transverse porous blocks, the pressure drop is not changed in these cases. Also, the highest thermal performance ratio is when the porous material is placed along the walls in a longitudinal direction.Originality/valueTo the best knowledge of the authors, in the previous research, the effect of the arrangement and location of the porous medium in the transverse and longitudinal direction in the microchannel and their effect in different states on the behavior of flow and heat transfer has not been numerically investigated. In this study, the porous media configuration and its placement in a 3D microchannel were numerically studied. The effect of porous material layout and configurations in different longitudinal and transverse directions on the pressure drop, heat transfer and thermal performance in the 3D microchannel is investigated numerically.