In this work, we present a facile yet effective method to prepare boron-doped, highly reduced electrochemical graphene oxide (B-rEGO) using electrochemical oxidation coupled with high-temperature thermal reduction. We first fabricated EGO from natural graphite powder in different concentrations of sulfuric acid electrolytes in a packed-bed reactor and found that the 12 M acid could produce EGO with the highest level of oxidation. To introduce heteroatom doping (non-metallic boron), sufficient boric acid was added to the sulfuric acid electrolyte for electrochemical reactions whereby the boron-doped graphene precursor could be formed, namely tetraborate anion intercalated EGO compounds, and it could transform into B-rEGO by annealing at 900 °C for 3 h under Ar gas. We found that the B-rEGO was highly defective as well as effectively deoxygenated and contained 0.21 at.% of boron. The as-prepared B-rEGO is used as an active material in sodium ion battery anodes, delivering a good capacity of 129.59 mAh g−1 at the current density of 100 mA g−1 and long-term cyclic stability which could retain 100.20 mA g−1 after 800 cycles at 500 mA g−1.