Background: Medicinal and aromatic plants play a significant role in drug discovery and development process. Flavonoids, revealing a wide spectrum of biological activities, extensively found in plants are important secondary metabolites. Materials and Methods: Aerial parts of Cyclotrichium origanifolium were collected, dried, and boiled in water then extracted with hexane, ethyl acetate, and n-butanol. Total phenolic content, DPPH· scavenging activity, reducing power (FRAP) activity, and ABTS·+ scavenging activity assays were applied for all extracts. The ethyl acetate extract revealing the most antioxidant activity as well as including the highest phenolic contents was subjected to chromatographic techniques (column chromatography, sephadex LH-20, semipreparative HPLC) to isolate the active compounds. The structure of isolated compounds were elucidated by spectroscopic methods (1D NMR, 2D NMR, and LC-TOF/MS). Results: Isosakuranetin (1), eriodictyol (2), luteolin (3), naringenin (4), and apigenin (5) were isolated and identified. All isolated flavonoids displayed the excellent antioxidant activity. Conclusion: The isolated flavonoids and also plant extract have potency to be a natural antioxidant.