Disclosed relates to an electrochemical determination system of glycated proteins, the system comprising: a filtering means for filtering labeled compounds bound to glycated proteins and non-glycated proteins after adding labeling compounds, capable of selectively binding to the glycated proteins to a solution, in which glycated/non-glycated proteins coexist, to be bound all to the glycated proteins; and a quantifying means for quantifying the filtered labeling compounds, not bound to the glycated proteins. The system of the present invention filters the residual labeled compounds left after binding to glycated proteins to quantify, instead of directly quantifying glycated proteins via the known glycated protein determination methods, thus simplifying the configuration of the system that can provide exact determinations with a low cost. Moreover, the electrochemical determination system of glycated proteins of the present invention minimizes the interference that the proteins are absorbed to an analysis device and a sensor in the system, not using immune antibodies that are expensive and have limited lives and, furthermore, not modifying the electrodes of the electrode sensor with antibodies or enzymes, thus facilitating mass production, quality control and circulation of the products.