Methyl jasmonate (MeJa) is an endogenous plant growth substance that regulates many aspects of plant development and growth, including chilling injury (CI) stress. Then, taking into account that pomegranate fruits are susceptible to CI, the main objective of this paper was to study the effect of MeJa on pomegranate fruit quality attributes during storage under chilling conditions. Pomegranates were treated after harvest with MeJa at two concentrations (0.01 and 0.1 mM), and then stored under chilling temperature for 84 days. Control fruits exhibited CI symptoms, manifested by pitting and browning, the severity being enhanced as storage time advanced, which were accompanied by softening and increase in electrolyte leakage (EL). The CI symptoms were significantly reduced by MeJa treatments, and total phenolic and anthocyanin concentration increased. Total antioxidant activity decreased in control arils, while increases occurred in arils from MeJa treated fruits. Results suggest that MeJa treatment has potential postharvest applications to reduce CI, maintain quality and improving the health benefits of pomegranate fruit consumption by increasing their content in bioactive compounds and antioxidant capacity.