The thermal performance of nanofluids in microchannel of rectangular cross-section was experimentally investigated in this study. In the previous studies, a threshold nanoparticle concentration exists where the critical concentration separates the heat transfer performance of the nanofluid during a flow through microchannels. Thus, the emphasis of our study is to find the optimum concentration value of nanoparticles for enhancing the forced convective heat transfer coefficients. In this study, thin-film thermocouple array (TFTA) of K-Type (Chromel/ Alumel) was employed to measure the temperature profile on the heated surface in the microchannel (while the top and wall was sufficiently insulated). The TFTA deposited on a silicon wafer is bonded with a polymer substrate containing the molded microchannel. The microchannel was made using the Poly Di-Methyl Siloxane (PDMS). The mold for the microchannel in order to cure the PDMS onto it was fabricated using soft-lithography technique on an atomically stable silicon substrate. To assess the thermal performance of nanofluids in micro-channels, the temperature profiles in the heated bottom wall of the micro-channel was monitored using the TFTA which was then used to estimate the wall heat flux values. The concentration and size of the silica nanoparticles in the aqueous nanofluids are parametrically varied in this study (e.g. at weight concentrations of 0.5%, 0.1% and 0.2%). These parametric experiments were performed by varying the wall temperatures (e.g. 30, 50 and 70 °C) and flow rates (e.g. 5, 7 and 9 μl/min).