The present paper is a numerical investigation on the performance of perforated baffles in a plate-fin heat exchanger. Two types of perforations are studied, namely the circular and elliptical shapes. Values of heat transfer coefficient, pressure drop, and thermal performance factor are determined for both cases and compared with those for a smooth channel. Also, the flow fields and heat transfer characteristics are determined for different fluids and various Reynolds numbers. The working fluids are complex, non-Newtonian and have an inelastic shear thinning behavior. The obtained results showed a good enhancement in the thermal performance factor by the suggested design in baffles. In the case of low viscous fluids, the elliptical perforated baffle performs better (by about 63.4%) than the circular one for all values of Reynolds number. But for highly viscous fluids, the elliptical perforation shows higher thermal performance than the circular hole by about 25% for low Reynolds numbers and 27% for high Reynolds numbers. The overall thermal performance factors are about 1.55 and 1.74 for the circular and elliptical perforations, respectively.