This study aims to investigate entropy generation for flow of three different nanofluids in a chaotic minichannel. Fluid particles in this channel move in chaotic trajectories, which can intensify the flow mixing. The results show that the contribution of heat transfer to entropy generation is greater than that of friction. With increasing the concentration, thermal entropy generation decreases for the alumina–water and Cu–water nanofluids, while intensifies for the magnetite–water nanofluid. With increase in Reynolds number for all nanofluids, thermal entropy generation decreases while frictional entropy generation increases. With the concentration increment, frictional entropy generation rate has an ascending trend for the alumina–water and magnetite–water nanofluids, while has a descending trend for the Cu–water nanofluid. Moreover, as Reynolds number increases from 50 to 200 at concentration of 1%, total entropy generation reduces 66.25%, 65.9% and 68.9% for the magnetite, alumina and Cu nanofluids, respectively. Based on the second law of thermodynamics, the Cu–water nanofluid is a more appropriate coolant owing to smaller total entropy generation. Moreover, use of the Cu–water and alumina–water nanofluids is more suitable at greater concentrations, while employing the magnetite–water nanofluid is only recommended at low concentrations.