The effect of the interior structure of carbon nanomaterials on their electrochemical properties is not well understood. We report here the electron transfer rate (ETR) of ferrocene (Fc) molecules covalently attached to the exposed end of carbon nanofibers (CNFs) in an embedded nanoelectrode array. The ETR in normal DC voltammetry was found to be limited by the conical graphitic stacking structure interior of CNFs. AC voltammetry, however, can cope with this intrinsic materials property and provide over 100 times higher ETR, likely by a new capacitive pathway. This provides a new method for high-performance electroanalysis using CNF nanoelectrodes.