Fermentation of foods by lactic acid bacteria is a useful way to improve the nutritional value of foods. In this study, the health-promoting effects of fermented papaya juices by two species, Lactobacillus acidophilus and Lactobacillus plantarum, were determined. Changes in pH, reducing sugar, organic acids, and volatile compounds were determined, and the vitamin C, total phenolic content, and flavonoid and antioxidant capacities during the fermentation process were investigated. Juices fermented by Lactobacillus acidophilus and Lactobacillus plantarum had similar changes in pH and reducing sugar content during the 48 h fermentation period. Large amounts of aroma-associated compounds and organic acids were produced, especially lactic acid, which increased significantly ( < 0.05) (543.18 mg/100 mL and 571.29 mg/100 mL, resp.), improving the quality of the beverage. In contrast, the production of four antioxidant capacities in the fermented papaya juices showed different trends after 48 hours' fermentation by two bacteria. Lactobacillus plantarum generated better antioxidant activities compared to Lactobacillus acidophilus after 48 h of fermentation. These results indicate that fermentation of papaya juice can improve its utilization and nutritional effect.