Liquid cooling systems in compact electronic devices prefer microchannel due to its large surface area to volume ratio. In the present study, three-dimensional numerical simulations are carried out to analyze the flow and heat transfer characteristics of sinusoidal wavy wall rectangular microchannel. The objective of this study is to disturb the thermal boundary layer by incorporating waviness in selective location which enhances heat transfer rate with the cost of minimum increase in total pressure drop. The coolants used in this study are water and nano-fluids (water + Al₂O₃; water + SiO₂; water + CuO) with the volume fraction of 4%. The study has been conducted by fixing the wavy parameters viz., wavelength (λ) and wave amplitude(A) of the bottom wall waviness. The effect of different working fluids on pressure drop and heat transfer enhancement is studied for the range of Reynolds number, 100 ≤ Re ≤ 1000. The water + CuO nano-fluid produces larger pressure drop among the chosen working fluids. Meanwhile water + Al₂O₃ shows better heat transfer enhancement. Further, the detailed analysis has been carried out using velocity and temperature distribution plots.