Black ginseng (BG), a traditional medicinal herb produced through a nine-stage steaming and drying process, exhibits stronger pharmacological efficacy, including antioxidant, anti-inflammatory, and anti-cancer properties, when compared to white and red ginseng. The ginsenosides in BG are classified as major and minor types, with minor ginsenosides demonstrating superior pharmacological properties. However, their low concentrations limit their availability for research and clinical applications. In this study, hot melt extrusion (HME) was utilized as an additional processing technique to enhance the content of minor ginsenoside in BG, and the physicochemical properties of the formulation were analyzed. Ginsenoside content in BG and HME-treated BG (HME-BG) was analyzed using high-performance liquid chromatography (HPLC), while their physicochemical properties were evaluated through dynamic light scattering (DLS), electrophoretic light scattering (ELS), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and Fourier-transform infrared spectroscopy (FT-IR). HME treatment resulted in a significant increase in minor ginsenosides Rg3 and compound K (CK) by 330% and 450%, respectively, while major ginsenosides Rg1 and Rb1 decreased or were not detected. Additionally, HME-BG demonstrated reduced particle size, improved PDI, and decreased crystallinity. HME treatment effectively converts major ginsenosides in BG into minor ginsenosides, enhancing its pharmacological efficacy and showing great potential for research and development applications.