The development of convenient and accessible health-functional foods has become an area of increased interest in recent years. Probiotics, ginseng, and yogurts have been recognized as representative nutraceutical products. To improve the functionality of yogurts, co-fermentation was performed during yogurt preparation. Four kinds of yogurt were prepared using a combination of probiotic Lactobacillus brevis B7 and hydroponic ginseng based on plain yogurt. The fundamental characteristics of yogurts, including pH, titratable acidity, microbial counts, color, and physicochemical properties, were determined. To assess functionality, four different antioxidant assays and real-time PCR analysis using RAW 264.7 cells were performed. Finally, sensory evaluation was conducted to evaluate customer preference. Hydroponic ginseng supplementation influenced pH, solid content, lightness, and yellowness. However, probiotic supplementation did not affect most factors except pH. In functionality analysis, the yogurt co-fermented with probiotics and ginseng showed the highest antioxidant activity and gene expression levels of the immune-related factors TNF-α and iNOS in RAW 264.7 cells. Although ginseng supplementation received poor acceptance because of its color and flavor, these attempts were considered beneficial despite the risk. Overall, co-fermentation within a short yogurt preparation time presented the potential for improvement of functionality. These findings suggest a range of feasibility for the development of attractive nutraceutical products.