Significant enhancement in supercapacitor performance was achieved via the synthesis of nanocrystalline RuO2 on vertically aligned Few Layered Graphene (FLG) nanoflakes, synthesized on bare n-type heavily doped silicon substrates by microwave plasma chemical vapour deposition. The RuO2 nanoparticles (diameter <2 nm) were deposited using a combination of low base pressure radio frequency magnetron sputtering and subsequent electrochemical cycling in acidic media. The well-dispersed RuO2 nanoparticles on FLGs achieve a specific capacitance of the order of 650 F g−1. The specific capacitance of RuO2–FLGs is significantly higher than pristine sputtered RuO2 (∼320 F g−1) and FLGs (∼6 F g−1) indicative of the synergistic effect between the FLGs and RuO2. In addition, the fabricated RuO2–FLG supercapacitors show excellent cycling capability with approximately 70% retention of initial specific capacitance over 4000 cycles at high charging–discharging rates of 500 mV s−1. The superior electrochemical performance is attributed to the good electronic conductivity of the FLGs as well as high utilization of well-dispersed RuO2 nanoparticles on FLGs.