In comparison with raw garlic, aged black garlic has been shown to display multiple pharmacological activities. We recently reported that pretreatment of pectinase cocktail with high hydrostatic pressure (HHP) before the process of aging garlic juice improves its antidiabetic activity and increases S-allylcysteine (SAC) content. Thus, this study was designed to investigate the influence of pectinase cocktail with HHP on the quality of aged black garlic juice formation and to identify the optimal manufacturing conditions. In the pretreatment step, garlic juice is heated at 55°C for 24 h. The contents of SAC and total polyphenols were increased with treatment of pectinase cocktail; this increase was greater under HHP processing. In contrast, the total flavonoid content was decreased in all pretreatment conditions. Garlic juice pretreated with pectinase cocktail and HHP had a significantly higher content of SAC in the early phase of aging than raw garlic juice, and the SAC was increased over time in both treatment groups. The total polyphenol content of garlic juice was significantly higher in the pretreatment group during the aging period, and the antioxidant activity of garlic juice showed a positive correlation with polyphenol content. Interestingly, HHP increased the enzymatic activity of the pectinase cocktail.