A micro-supercapacitor with a three-dimensional configuration has been fabricated using an ICP etching technique. Hydrous ruthenium oxide with a tubular morphology is successfully synthesized using a cathodic deposition technique with a Si micro prominence as a template. The desired tubular RuO2·xH2O architecture facilitates electrolyte penetration and proton exchange/diffusion. A single MEMS electrode is studied using cyclic voltammetry, and a specific capacitance of 99.3 mF cm−2 and 70 F g−1 is presented at 5 mV s−1 in neutral Na2SO4 solution. The accelerated cycle life is tested at 80 mV s−1, and satisfactory cyclability is observed. When placed on a chip, the symmetric cell exhibits good supercapacitor properties, and a specific capacitance as high as 23 mF cm−2 is achieved at 10 mA cm−2. Therefore, 3D MEMS microelectrode arrays with electrochemically deposited ruthenium oxide films are promising candidates for on-chip electrochemical micro-capacitor applications.