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Abstract Background Ephedra chilensis K Presl, known locally as pingo–pingo, is a Chilean endemic plant used in traditional medicine as an anti-inflammatory and used in other treatments. However, unlike for the other Ephedra species, there have been no reports on the antioxidant and cytotoxic effects of this plant. The present study aims to explore the potential applications of E. chilensis extract as a cytotoxic agent against in vitro cancer cell lines and to explore the relationship between this extract and antioxidant activity. Methods Total anthraquinone, flavonoid, and phenolic contents, as well as antioxidant activity (DPPH, FRAP, and TRAP assays) and cytotoxic effect on several cancer cell lines (MCF-7, PC-3, DU-145, and HT-29) were measured for the hexane, dichloromethane and ethanol extracts of E. chilensis. In addition, several correlations among the phytochemical content, antioxidant activity, and cytotoxic effect were evaluated. Finally, GC-MS analyses of the most active extracts were carried out to identify their major components and to relate these components to the cytotoxic effect. Results Antioxidant activity was found in the EtOH extracts of Ephedra, and the results were correlated with the phenolic content. For the cytotoxic activity, the non-polar extracts of E. chilensis had the highest antiproliferative effect for the MCF-7 and PC-3 cancer lines; the extract was shown to be up to three times more selective than doxorubicin. However, the cytotoxic effect was not correlated with the antioxidant activity. Lastly, the GC-MS analysis showed a high concentration of saturated fatty acids (mainly n-hexadecanoic acid) and terpenoids (mainly 4-(hydroxy-ethyl)-γ-butanolactone). Conclusion The cytotoxic activity and selectivity of the non-polar extracts of E. chilensis for the MCF-7 and PC-3 cell lines could be related to the terpenic compounds and fatty acids of the extracts or to the synergistic effect of all of the compounds in the extracts. These non-polar extracts can be used for the development of new drugs against breast and prostate cancer.