Focused electron beams with high energy acceleration are versatile probes. Focused electron beams can be used for high-resolution imaging and multi-mode nanofabrication, in combination with, molecular precursor delivery, in an electron microscopy environment. A high degree of control with atomic-to-microscale resolution, a focused electron beam allows for precise engineering of a graphene-based field-effect transistor (FET). In this study, the effect of electron irradiation on a graphene FET was systematically investigated. A separate evaluation of the electron beam induced transport properties at the graphene channel and the graphene-metal contacts was conducted. This provided on-demand strategies for tuning transfer characteristics of graphene FETs by focused electron beam irradiation.