While bio-oil-derived fuels hold much promise as a replacement for petroleum, transformation of the highly oxygenated mixture has proven challenging. In particular, bio-oils are reactive and difficult to upgrade through catalytic pyrolysis. To reach a stabilized product capable of deep deoxygenation at elevated pressure and temperature, conversion or separation of reactive groups is required. This paper describes an electrochemical process for stabilization and upgrading of bio-oils prior to hydrotreating at high pressure and temperature. This electrolytic process uses a three-compartment cell designed to hydrogenate reactive carbonyl components while separating small acid molecules, such as acetic and formic acids, which act as catalysts for condensation reactions and consume hydrogen gas to produce low-value gases in hydrotreating. To avoid conductivity issues, electrodes are appended to anion- and cation-exchange membranes. The cell was tested using a mixed acetic acid and formic acid surrogate fed to the cathode compartment, where the decrease in the concentration followed the applied charge to the cell. Experiments performed using pine pyrolysis oil demonstrated a significant reduction in the total acid number (TAN), an increase in pH from 2.6 to over 4, and a modest reduction of the carbonyl concentration. Analysis showed the reduction in TAN was primarily due to removal of carboxylic compounds. Experiments observed a decrease in the reactive carbonyl (aldehydes and ketones) concentration that followed applied charge. The results with the newly devised reactor show promise for the electrochemical route for upgrading bio-oils, but significant improvements in TAN removal and carbonyl conversion are needed. Given the distributed nature of biomass, an electrochemical process paired with pyrolysis could be used to densify and stabilize an oil product near the source. The densified liquid could then be shipped to centralized refineries for final upgrading to fuel and/or chemical products.