Interdigitated carbon micro-electrode arrays for micro-capacitors are fabricated through the carbon microelectromechanical systems (C-MEMS) technique which is based on the carbonization of patterned photoresist. To improve the capacitive behavior, electrochemical activation is performed on carbon micro-electrode arrays. Cyclic voltammetry (CV) and galvanostatic charge–discharge results demonstrate that the electrochemical activation effectively increases the capacitance of the micro-electrode arrays by three orders of magnitude. Although the charge–discharge experiments show the non-ideal behavior of micro-capacitors, the specific geometric capacitance reaches as high as 75mFcm−2 at a scan rate of 5mVs−1 after electrochemical activation for 30min. The capacitance loss is less than 13% after 1000 CV cycles. These results indicate that electrochemically activated C-MEMS micro-electrode arrays are promising candidates for on-chip electrochemical micro-capacitor application.