Plant roots, leaves, barks, seeds berries or flowers can be used to promote health and treat diseases and also have compounds that provide information about the best quality of a raw materials. A medicinal plant native to the Amazonia region (Brazil) was investigated in this work. For this purpose, a new analytical approach was developed by capillary zone electrophoresis (CZE) with UV detection for the separation of 14 phenolic compounds extracted from the plant extracts. The method enabled simultaneous determination of 3-acetylcoumarin, resveratrol, 6-hydroxycoumarin, catechin, rutin, ferulic acid, quercitrin, kaempferol, fisetin, myricetin, quercetin, caffeic acid, gallic acid and 4-hydroxycinnamic acid using borate buffer (20 mM, pH 9.2) containing 15% methanol (v/v) as working electrolyte, separation potential of–20 kV, separation temperature of 25 °C and hydrodynamic injection by gravity (20 cm for 60 s). The developed method was validated, obtaining repeatability and inter day precision values lower than 7% and 6%, respectively. Recovery was performed and ranged from 84% to 118%. The method permitted the quantification of catechin and rutin in Connarus perrottetii var. angustifolius aqueous infusions, ethanolic extracts and butanolic extracts (both obtained after maceration). The radical scavenging activity of the extracts towards free radicals is also described.