Continuous glucose monitoring (CGM) systems are most important in the current Type I diabetes care and as component for the development of artificial pancreas systems because the amount of insulin being supplied is calculated based on the CGM results. Therefore, to stably and accurately control the blood glucose level, CGM should be stable and accurate for a long period. We have been engaged in the biomolecular engineering and application of FAD dependent glucose dehydrogenase complex (FADGDH) which is capable of direct electron transfer. In this study, we report the development of the third-generation type open circuit potential (OCP) principle-based glucose sensor with direct electron transfer FADGDH immobilized on gold electrodes using a self-assembled monolayer (SAM). We developed a novel algorithm for OCP-based glucose sensors. By employing this new algorithm, high reproducibility of measurement and sensor preparation were achieved. In addition, the signal was not affected by the presence of acetaminophen and ascorbic acid in the sample solution. The thus optimized third-generation OCP-based glucose sensor could be operated continuously for more than 9 days without significant change in the signal, sensitivity and dynamic range, indicating its potential application for CGM systems.