Abstract Bioenergy sources are being advanced as a meaningful environmental solution and a substitute for conventional energy sources. Bioenergy from biomass feedstocks currently comprises the largest portion of renewables in the United States. Thus, more effective process-level solutions can result in scaling-up biomass-derived energy production (e.g., biofuels). Pyrolysis, a thermochemical conversion technology, offers a commercially viable pathway to produce bio-oil from a wide range of biomass feedstocks (e.g., algae and terrestrial). Bio-oil requires further upgrading to produce final bioproducts (e.g., transportation fuels and biochemicals). This article focuses on the upgrading of bio-oil to transportation fuels (liquid hydrocarbons), highlights the critical challenges of existing upgrading technologies, and identifies the potential research directions to meet the market needs. A comprehensive overview and classification of bio-oil upgrading pathways and their competencies are presented through both comparative and systematic literature reviews. It is concluded that the biofuel production cost is highly dependent on post-conversion pathways, particularly their hydrogenation and deoxygenation capacity. Thermochemical treatments are effective, but less cost-competitive due to the intensive process requirements (e.g., heat or pressure). Biochemical treatments are inadequate as a standalone process for upgrading bio-oil. Physicochemical treatments are less effective, however, they operate under mild process conditions and could be integrated with other treatments. It is further concluded that the electrochemical approach can be effective due to the retention of hydrogen from bio-oil water content during deoxygenation.