This study explores the influence of different fluids in a uniform micro-channel geometry on conjugate heat transfer. Nanofluids used here, are SiO2 and Al2O3 nanoparticles with various concentrations up to 4% in water as a base fluid under laminar flow. Nanofluids are compared to an ionic liquid called Butyl Methyl Imidazolium Tetrafluroborate (BMIM BF4) to examine the influence of heat transfer and fluid flow characteristics. Good agreement was found against previous micro-channel studies, numerical simulations with COMSOL Multiphysics® V5.2a are used at Reynolds number ranging from 50 to1000 with a uniform heat flux of 100 W/cm2 relevent to cooling systems. Advanced fluids might offer significant potential in combatting the challenges of heat transfer in the technological drive toward lower weight/smaller volume electrical and electronic devices. The results show that the lowest thermal resistance is for nanofluids followed by water, then the ionic liquid. Moreover, Al2O3-water offers lower thermal resistance than the SiO2-water for all given nanoparticle concentrations. It is also found that there is no beneficial using ionic liquids in forced convection systems which work below boiling temperature conditions.