Stem cell therapy (SCT) has emerged as a promising regenerative approach in the management of complex orthopedic conditions and orthodontic alveolar bone remodeling. Mesenchymal stem cells (MSCs) derived from bone marrow, adipose tissue, and other sources possess the ability to differentiate into osteogenic lineages and modulate inflammation, facilitating endogenous repair mechanisms. This systematic review consolidates recent clinical and preclinical evidence regarding the safety, efficacy, and mechanisms of SCT in orthopedic bone regeneration and alveolar bone remodeling during orthodontic treatment. Results demonstrate significant enhancements in bone healing rates, function, and structural restoration, although challenges remain regarding optimal delivery, standardization, and long-term outcomes. Future directions involve advanced biomaterials, gene editing, and personalized medicine to refine therapeutic protocols.