Bone defects challenge human health, highlighting the need for new therapies. This research aims to develop and characterize a PCL/PAN/casein (PCL/PAN/CA) scaffold and to assess the attachment, growth, and differentiation of endometrial stem cells (EnMSCs) into osteoblasts for potential use in bone tissue engineering (BTE). In this study, 0.5 g of PCL and PAN were individually dissolved in 5 mL of DMF and electrospun to prepare PAN and PCL scaffolds. The nanofiber surfaces were then coated with casein. The scaffolds’ chemical characteristics were examined through scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier transform infrared (FTIR) techniques. Additionally, the biocompatibility and cytotoxicity of the scaffolds on EnMSCs were evaluated through the MTT test, acridine orange staining, and DiI labeling. The differentiation of osteoblasts on the synthesized scaffolds and the role of casein in cell growth and differentiation were examined. Additionally, Masson’s trichrome staining was utilized to assess the healing process of bone lesions in rat models after scaffold grafting. The results indicated that the fabricated scaffolds exhibited a nanofibrous structure, with diameters of 370 nm for PCL, 250 nm for PAN, and 290 nm for PAN/PCL. The PAN/PCL/CA scaffold showed the most significant osteoblast proliferation and differentiation levels. In animal studies, grafting the PCL/PAN/CA scaffold led to a 31% improvement in recovery compared to the control group and the PCL/PAN scaffold on its own. The PAN/PCL/CA scaffold demonstrated a remarkable capacity to facilitate the proliferation, growth, and differentiation of EnMSCs, underscoring its promising suitability for applications in BTE.