In the present work we develop an electrochemical assisted method to form nanopores on the surface of highly oriented pyrolytic graphite (HOPG), which was accomplished by a simple electrochemical route and a scalable nanomaterial, carbon nanodots, without applying high voltages, high temperatures or toxic reagents. HOPG electrodes are in a solution of N-enrich carbon nanodots in acidic media and the potential scans applied on HOPG lead to the formation of a spatially inhomogeneous porous surface. The diameter of the resulting nanopores can be tuned by controlling the number of electrochemical reduction cycles. The resulting nanoporous surfaces are characterized by atomic force microscopy, Raman spectroscopy, scanning electrochemical microscopy, electrochemical impedance spectroscopy and electrochemistry. These nanoporous HOPG showed high capacitance. Hence the potential of these surfaces to the development of energy storage devices is demonstrated.