The effect of pulsed electric fields on the polyphenol profile of tomato juices was studied. First, tomatoes were subjected to moderate-intensity pulsed electric fields (MIPEFs) and then were immediately refrigerated at 4 °C for 24 h. Treated and untreated juices were then subjected to high-intensity pulsed electric fields (HIPEFs) or thermal treatment (90 °C for 60 s). In comparison to references, tomatoes subjected to MIPEF treatments led to juices with a higher content of polyphenol compounds. A slight decrease in polyphenol compounds was observed over time in thermal- and HIPEF-treated juices, with the exception of caffeic acid. However, HIPEF-processed tomato juices had a higher content of polyphenol compounds (ferulic acid, caffeic-O-glucoside acid, p-coumaric acid, chlorogenic acid, rutin, and naringenin) just after processing and through storage than those thermally treated. Therefore, the combination of MIPEFs and HIPEFs could be proposed as a strategy for producing tomato juices with a higher content of phenolic compounds.