Copao (Eulychnia acida Phil., Cactaceae) is an endemic species occurring in northern Chile. The edible fruits of this plant are valued for its acidic and refreshing taste. Phenolic-enriched extracts from copao fruit pulp and epicarp, collected in the Elqui and Limari river valleys, were assessed by its in vitro ability to inhibit the pro-inflammatory enzymes lipoxygenase (LOX) and cyclooxygenases (COX-1 and COX-2). At 100 μg/mL, pulp extracts showed better effect towards LOX than epicarp extract, while COX-2 inhibition was observed for both epicarp and pulp samples. In general, the extracts were inactive towards COX-1. A positive correlation was observed between the anti-inflammatory activity and the main phenolic compounds found in this fruit. Copao fruits from the Limari valley, a main place of collection and commercialization, showed major activity, adding evidence on the possible health-beneficial effects of this native Chilean fruit.