This study was designed to investigate chemical composition, the total phenolic content, flavonoid content, antioxidant activity and to analyze through FT-IR spectroscopy method the freeze-dried extract of Ecballium elaterium fruit from three different localities. The highest level of phenolic and flavonoid contents was recorded for the fruit juice from the Cap-Bon region, with 106.4 ± 0.4 mg GAE/g and 6.5 ± 0.2 mg QE/g, respectively. Antioxidant activity varied in dose-dependent manner with IC 50 values for DPPH scavenging of the freeze-dried fruit juice extracts from Cap-Bon, Kef and Sidi Bouzid were 38.6 ± 0.2, 50.1 ± 0.7, and 50.7 ± 0.2 µg/mL, respectively. The results from the FRAP test showed that the freeze-dried extracts of Cap-Bon exhibited potent activity, followed by those from Kef and Sidi Bouzid. Similar trend were revealed for ABTS•+ test, with the fruit juice extract from Cap-Bon (IC 50 = 0.6 ± 0.0 mg/mL). Furthermore, a good positive correlation was observed between the total phenols and three assays, especially DPPH. The freeze-dried extracts of fruit juice from Cap-Bon showed strong ability to act as antioxidants and can be considered as promising natural source of bioactive compounds. FT-IR analysis of each freeze-dried extract confirmed its richness on polyphenols and biological active functional groups.