A Nano biofuel cell employing a Boron nitride nanotube (BNNT) and flavin adenine dinucleotide (FAD) based on the direct electron transfer principle has been investigated using HF and DFT theoretical methods. FAD was immobilized on the BNNT together by combining water molecules in box model. We have performed the quantum chemical model to evaluate the effect of BNNT in direction of electron transfer, stability, electric properties including resistance, voltage, current, conductivity, limiting conductivity, power and nuclear magnetic resonance parameters and thermochemical properties as a biofuel cell. The data exhibited that the BNNT biofuel cell model can be applied for generating electric power in lower resistances with the best agreement in linear correlation of voltage-current directly from sustainable fuel substrate such as FAD. In this paper, the results illustrated that together with the feasibility of using BNNT and FAD to become the norm in electrochemical bio system applications.