: Concerns over the exponential increase in the heat produced per unit area in electronic chips have driven advanced research into the nanofluid capability as a coolant. Generally reported for its improved thermal conductivity in particular at higher concentrations, different types of surfactant normally added used to stabilize the nanofluid have reported different thermal resistance to heat flow. This paper reports an analysis of the thermal performance of a nanofuid-cooled microchannel heat sink (MCHS) with 0.1% volume fraction of CNT nanofluid utilizing two different surfactants; Lignin (N2) and sodium polycarboxylate (N3) as stabilizers. Multi-objective particle swarm optimization (MOPSO) algorithm was utilized to simultaneously minimize the thermal resistance and pumping power by optimizing the design parameters; the wall width and channel aspect ratios. Optimization outcomes showed that the thermal resistance of CNT nanofluids is lower than water by 1% at 20°C. Nanofluid with N3 has a significantly higher pressure drop than water, up to 47%. CNT nanofluid with N3 performed poorly due to the high viscosity which consequently results both in higher thermal resistance and pressure drop. Since a surfactant alters the properties of nanofluid, it could improve or deteriorate the performance of a MCHS overall and must not be taken lightly as a MCHS is expected to operate for a long time.