Biofuels have gained much attention as a potentially sustainable alternative to fossil fuels to tackle climate change and energy scarcity. Hence, the increasing global interest in contributing to the biofuel supply chain (BSC), from biomass feedstock to biofuel production, has led to a huge amount of scientific production in recent years. In this vein, techno-economic analysis (TEA) of biofuel production to estimate total costs and revenues is highly important for transitioning towards a bioeconomy. This research aims to provide a comprehensive image of the body of knowledge in TEA evolution within the BSC domain. To this end, a systematic science mapping analysis, supported by a bibliometric analysis, is carried out on 1104 articles from 1986 to 2021. As a result, performance indicators of the scientific production within the target literature are presented to explain how this literature has evolved. Besides, thematic trends and conceptual structures of TEA of biofuel production are discovered. The results show that (i) biofuel production and consumption need promotion through tax measures and price subsidies, (ii) the development of cost-competitive algal biofuels has faced many challenges over recent years, and (iii) TEA of algal biofuels to identify commercial improvements and increase the economic feasibility is still lacking, which calls for more in-depth investigations. Consequently, current challenges and future perspectives of TEA in the BSC domain are rendered. The provided insights enable researchers and decision-makers involved in BSCs to (i) capture the most influential contributors to the field and (ii) identify major research hotspots and potential directions for further development.