Using single layer microchannels accompanied by nanofluids is one of the most practical solutions in thermal management of high power density devices. The main challenge in cooling systems of electronic devices is to provide a uniform temperature distribution. In the present study, fluid flow and heat transfer in a fractal microchannel heatsink have been simulated employing the computational fluid dynamics (CFD) method. The fractal microchannel is used to achieve uniform temperature distribution. Thermal performance of single-walled carbon nanotubes (SWCNT) and multi-walled carbon nanotubes (MWCNT) dispersed in the two base fluids of water and kerosene in a fractal microchannel at Reynolds (Re) numbers of 1500 to 3000 are investigated. It should be noted that the nanofluids have been simulated by the two-phase mixture model. The results indicated that the use of fractals silicon microchannel leads to having a uniform temperature distribution. Based on the results, at maximum Re number when the working fluid is water, Nu number and pumping power are 20.9 and 0.033 W whereas, in kerosene flow at the same condition, Nu number and pumping power are 6 and 0.054 W, respectively. According to the obtained results, using the SWCNT nanoparticle compared with the MWCNT nanoparticle leads to a significant enhancement in the Nusselt (Nu) number. This difference is more pronounced by increasing the Re number and nanoparticle volume fraction. In addition, the results indicated that at the same Re number and nanoparticle volume fraction, the performance evaluation criterion of the water-based nanofluid is 4 times higher than that of the kerosene-based nanofluid. So the use of the water as the working fluid with the SWCNT nanoparticle for cooling in the fractal silicon microchannel is recommended.