Background: Facial reconstruction represents one of the main challenges for surgeons. Stem cells (SC) represent the most studied solution for tissue regeneration. This approach appears particularly promising in combination with bioengineered scaffolds and 3D bioprinting. The purpose of this systematic review is to define the main domains of current application of SC therapy within contemporary clinical workflows, evaluate indications and limitations, report current knowledge in this innovative field of research, and define the landscape of evidence for such approaches. Methods: A systematic review was performed on the pertinent literature regarding stem cell-based cell therapies currently available in the reconstruction of the face. The review used the main databases for scientific literature based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: A total of 15 papers were selected after an independent search was performed. The two major domains for current application of stem cells in clinical practice were bone and skin categories. Conclusions: Cell therapy in the field of facial reconstruction represents a promising approach. The evidence regarding the current clinical use, however, seems to show this option to be limited. Bioengineering advances and the parallel development of 3D bioprinting technology can potentially enhance the role of stem cells in the future.