Osteoporosis, characterized by an increased risk of fractures, represents a significant global public health issue. Natural compounds have emerged as promising candidates for addressing this condition. Shikonin, derived from Lithospermum erythrorhizon as a purple-red naphthoquinone pigment, exhibits a diverse array of biological activities, including antibacterial, anti-inflammatory, and anticancer properties. Despite the well-documented bone-protective properties of shikonin, the precise molecular mechanisms underlying its role in the differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) into osteoblasts, along with its implications on angiogenesis, are not fully elucidated. Our study showcases shikonin's ability to stimulate the differentiation of BMSCs into osteoblasts, leading to an upregulation of osteoblast-specific marker genes such as OC, Runx2, BMP2, and ALP. Furthermore, shikonin intervention triggers the upregulation of phosphorylation of p38, ERK, and JNK in the MAPK signaling pathway. Furthermore, shikonin has been shown to enhance the migration and angiogenic capabilities of human umbilical vein endothelial cells (HUVECs). Notably, the augmentation of HUVEC migration by shikonin can be counteracted by the addition of a JNK inhibitor. Furthermore, our findings indicate that shikonin effectively improves osteoporosis in aged mice by promoting osteoblast differentiation. In summary, our study elucidates the molecular mechanisms through which shikonin exerts its beneficial effects in the treatment of osteoporosis, highlighting its potential as a novel therapeutic option for both the prevention and management of this condition.