The effect of moderate intensity pulsed electric fields (MIPEF) on the bioactive compounds (total polyphenol, lycopene, and vitamin C content) as well as on the antioxidant capacity of tomato fruit was studied. The MIPEF treatment conditions were optimized to obtain tomato fruit with a high content of bioactive compounds. Tomato fruits were subjected to different electric field strengths (from 0.4 to 2.0 kV/cm) and number of pulses (from 5 to 30) and then immediately refrigerated at 4 °C for 24 h. A concentration of bioactive compounds higher than that of untreated tomatoes was obtained in MIPEF-treated tomatoes. A 44% increase in total polyphenol content was achieved under 30 pulses at 1.2 kV/cm. The hydrophilic antioxidant capacity was also enhanced by 44% applying 18 pulses at 1.2 kV/cm, and the lipophilic antioxidant capacity was increased by 37% under 5 pulses at 1.2 kV/cm. The maximum overall level of bioactive compounds and antioxidant capacity in the treated tomatoes was obtained under 16 pulses at 1 kV/cm. Therefore, MIPEF treatments could be considered an effective method to enhance the bioactive compound content and antioxidant potential of tomatoes.