Increasing the thermal conductivity of PDMS (polydimethylsiloxane) based microfluidics is an important issue for the thermal management of hot spots produced by embedding electronic circuits in such systems. This paper presents a solution for enhancing the thermal conductivity of such PDMS based microfluidics by introducing thermally conductive alumina (Al2O3) nanoparticles, forming PDMS/Al2O3 nanocomposites. The materials are fully characterized for different concentrations of Al2O3 in PDMS for experiments which are conducted at different flow rates. Our results suggest that incorporation of Al2O3 nanoparticles at 10% w/w in the PDMS based nanocomposite significantly enhances the heat conduction from hot spots by enhancing the thermal conductivity, while maintaining the flexibility and decreasing the specific heat capacity of the developed materials. This proof-of-concept study offers potential for a practical solution for the cooling of future embedded electronic systems.