Rare-earth elements (REEs) are critical components of low-carbon technologies and advanced defense systems. However, their conventional extraction and separation processes, which rely on energy-intensive hydrometallurgy with harsh chemical reagents, pose significant environmental challenges. Synthetic biology offers a transformative alternative by enabling the programmable dissolution, precise molecular recognition, and selective capture of REEs under mild conditions. Specifically, engineered microbes can be designed to secrete tailored organic acids, siderophores, and redox-active metabolites for bioleaching REEs from ores, tailings, and industrial wastes. Concurrently, high-affinity biological binders—such as lanmodulin, lanthanide-binding peptides, and de novo-designed proteins—provide picomolar-level affinity and tunable selectivity ideal for biosorption. The integration of these functional motifs into advanced platforms, including immobilized sorbents, magnetic composites, and elastin-like polypeptides, enables continuous and regenerable REE recovery with minimal chemical input. Collectively, these biological strategies support an environmentally considerable approach to REE extraction and separation from diverse sources. Future efforts should focus on machine-learning-guided protein design, enhancing biomolecule stability, developing integrated leaching-adsorption bioreactors, improving tolerance to complex leachates, and incorporating biological modules into industrial flowsheets. These advances collectively establish synthetic biology as the foundation for a new paradigm in sustainable rare-earth production.