Abstract Bio-jet fuel is increasingly being produced from feedstocks such as algae and tested in flight. As the industry adopts bio-jet fuels from various feedstocks and conversion processes, life cycle assessment (LCA) is necessary to determine whether these renewable fuels result in lower life cycle greenhouse gas (LC-GHG) emissions than conventional jet fuel. An LCA was performed for a functional unit of 1 GJ of bio-jet fuel produced through thermochemical conversion (hydrothermal liquefaction (HTL)) of microalgae cultivated in wastewater effluent. Two pathways were analyzed to compare the impacts of siting HTL at a wastewater treatment plant (WWTP) to those of siting HTL at a refinery. Base cases for each pathway were developed in part using primary data from algae production in wastewater effluent and HTL experiments of this algae at the University of Kansas. The LC-GHG emissions of these cases were compared to those of conventional jet fuel, and a sensitivity analysis and Monte Carlo analyses were performed. When algal conversion using HTL was modeled at a refinery versus at the WWTP site, the transportation steps of biomass and waste nutrients were major contributors to the LC-GHG emissions of algal bio-jet fuel. The LC-GHG emissions were lower for the algal bio-jet fuel pathway that performs HTL at a WWTP (35.2kg CO2eq/GJ for the base case) than for the pathway for HTL at a refinery (86.5kg CO2eq/GJ for the base case). The LCA results were particularly sensitive to the extent of heat integration, the source of the heat for HTL, and the solids content of dewatered algae. The GHG emissions of algal bio-jet fuel can be reduced by 76% compared to conventional jet fuel with feasible improvements in those sensitive parameters and siting HTL at a WWTP. Therefore, it is critical that transportation logistics, heat integration of biomass conversion processes, and nutrient supply chains be considered as investment and production of bio-jet fuels increase.