The application of HIPEF processing (35kV/cm for 1727μs using bipolar pulses of 4-μs at 188Hz) on watermelon juice was evaluated as an alternative to conventional heat treatments (90°C for 30s or 90s) in order to achieve better preservation of watermelon aroma compounds for 56days of storage at 4°C. HIPEF processing not only induced a rise (roughly 20%) in the concentrations of hexanal, (E)-2-nonenal, nonanal, 6-methyl-5-hepten-2-one and geranylacetone but also achieved less reductions on the retention of volatiles than the thermal treatment at 90°C for 60s. In contrast, the content of (Z)-6-nonenal, 1-nonanol and (Z)-3-nonen-1-ol in the untreated and processed juices remained unchanged after processing. Despite the decrease in overall flavor compounds observed during storage irrespective of the treatment applied, HIPEF-treated juices showed better flavor retention than heat-treated samples for at least 21days of storage. Moreover, changes in aldehydes and ketones during storage of treated watermelon juices were well fitted by a model based on the Weibull distribution function. Therefore, the application of HIPEF may be appropriate to preserve the initial volatile profile of watermelon juices during storage.