The effects of high-intensity pulsed electric field (HIPEF) processing (35 kV/cm for 1727 μs applying 4-μs pulses at 188 Hz in bipolar mode) on color, viscosity and related enzymes in watermelon juice were evaluated during 56 days of storage and compared to thermal treatments (90 °C for 60 s or 30 s). HIPEFtreated juice maintained brighter red color than thermally treated juices along the storage time. In addition, the application of HIPEF as well as heat at 90 °C for 60 s led to juices with higher viscosity than those untreated for 56 days of storage. On the other hand, peroxidase (POD) was inactivated more efficiently after HIPEF processing than after applying heat treatments. However, the thermally processed juice at 90 °C for 60 s kept the lowest residual POD activity values beyond day 7 of storage. Differences in lipoxygenase (LOX) activity among treatments were not appreciated at day 0. However, storage time had a strong reducing influence on the enzyme activity of heat-treated samples. A substantial loss of pectin methylesterase (PME) activity (more than 50%) was observed in all the treated juices, whereas a slight reduction in polygalacturonase (PG) activity was only achieved after the HIPEF treatment. The use of HIPEF technology could be an alternative to thermal treatments and could contribute to better maintain valuable attributes of watermelon juice. Industrial Relevance: HIPEF processing is a feasible alternative to thermal treatments to obtain watermelon juice, achieving optimal inactivation of deleterious microorganisms and quality-related enzymes. HIPEFtreated watermelon juices exhibit better physical properties such as color or viscosity than thermally treated juices throughout storage. Thus, HIPEF technology can help processors to obtain juices that keep their fresh characteristics, thus being better accepted by consumers.