In recent years, rare earth elements (REEs) have been widely used in various modern technological devices and the global demand for REE has been increasing. The increased demand for REEs has led to environmental exposure or water pollution from rare earth metal mines and various commercial products. Therefore, the development of a safe technology for the separation and adsorption of REEs is very important from the perspective of green chemistry and environmental pollution. In this review, the application and mechanisms of microorganisms for the removal and extraction of REEs from aqueous solutions are described. In addition, the advantages in using microorganisms for REE adsorption and future studies on this topic are discussed.