The effect of high intensity pulsed electric fields (HIPEF) processing (35 kV/cm for 1500 μs in bipolar 4-μs pulses at 100 Hz, with an energy density of 8269 kJ/L) on the main bioactive compounds and antioxidant capacity of tomato juice was investigated and compared to heat pasteurization (90 °C for 1 min or 30 s) having the fresh juice as a reference. HIPEF and heat treated tomato juices showed higher lycopene and lower vitamin C levels than the untreated juice. However, no significant changes in the total phenolic content and antioxidant capacity were observed between treated and fresh juices just after processing. Lycopene, vitamin C and antioxidant capacity of both treated and untreated juices decreased exponentially during storage following a first order kinetics (R2= 0.763–0.987), whereas tomato juices maintained their initial phenolic content. HIPEF-treated tomato juice maintained higher lycopene and vitamin C content than the thermally treated juices during the storage time. Hence, the application of HIPEF may be appropriate to achieve nutritious and fresh like tomato juice.