Abstract A new cooling technique for concentrator photovoltaic (CPV) systems is developed using various configurations of microchannel heat sinks. Five distinct configurations integrated with a CPV system are investigated, including a wide rectangular microchannel, a single layer parallel- and counter- flow microchannel, and a double layer parallel- and counter- flow microchannel. A comprehensive, three-dimensional thermo-fluid model for photovoltaic layers, integrated with a microchannel heat sink, is developed. The model is numerically simulated and validated using the available experimental and numerical data. Based on the results, the temperature contours on a plane located at the mid-thickness of the silicon layer are presented at different operating conditions and heat sink configurations. Accordingly, the maximum local temperature can be detected and temperature uniformity can be accurately estimated. Furthermore, at a concentration ratio of 20, the CPV system integrated with a single layer parallel- flow microchannel heat sink configuration (B) achieves the highest cell net power, electrical efficiency, and the minimum cell temperature. On the contrary, at the same operating conditions, the use of a single layer counter-flow microchannel heat sink configuration (C) is found to be the least effective cooling technique. The results of this study can guide industrial designers to adopt compact heat sink configurations and simple designs in the manufacturing process of hybrid CPV-thermal systems.