Cell-based therapy (CBT) is a revolutionary approach for curing a variety of degenerative diseases. Stem cell-based regenerative medicine is a novel strategy for treating tissue damages regarding stem cells unique properties such as differentiation potential, paracrine impacts, and self-renewal ability. However, the current cell-based treatments encounter considerable challenges to be translated into clinical practice, including low cell survival, migration, and differentiation rate of transplanted stem cells. The poor stem cell therapy outcomes mainly originate from the unfavorable condition of damaged tissues for transplanted stem cells. The promising method of preconditioning improves cell resistance against the host environment's stress by imposing certain conditions similar to the harsh microenvironment of the damaged tissues on the transplanted stem cells. Various pharmacological, biological, and physical inducers are able to establish preconditioning. In addition to their known pharmacological effects on tissues and cells, these preconditioning agents improve cell biological aspects such as cell survival, proliferation, differentiation, migration, immunomodulation, paracrine impacts, and angiogenesis. This review focuses on different protocols and inducers of preconditioning along with underlying molecular mechanisms of their effects on stem cell behavior. Moreover, preclinical applications of preconditioned stem cells in various damaged organs such as heart, lung, brain, bone, cartilage, liver, and kidney are discussed with prospects of their translation into the clinic.