The circular bioeconomy (CBE) is an increasingly popular method used to add value to bio-based products. However, these products entail impacts on sustainability that can be assessed by life cycle thinking (LCT). Therefore, this manuscript aims to describe the current development of using LCT for a CBE and to identify challenges and future perspectives with regard to this topic. A systematic literature review was conducted using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA), analyzing a final portfolio of 57 documents. The results indicated that the use of LCT for a CBE is very recent and has been increasing over the years, is concentrated in Europe, and mainly assesses the conversion of biowastes in biofuels through biorefinery processes, considering mostly environmental concerns, by applying life cycle assessment; thus neglecting economic and social issues. The use of system boundaries, software, databases, and impact assessment methods was reviewed. Five challenges were revealed (the expansion of system boundaries, the consideration of more endpoints, the development and use of regional databases, the development of policies to encourage CBE, and the addition of economic and social issues. Future perspectives will be aimed at considering microalgae, wastewater, and animal biomass in CBE processes, developing more value-added bioproducts and biofuels, and adding cost assessment and more circularity to CBE processes.