Origanum vulgare, a popular flavoring herb, is valued for several biological properties. The present study focused on the chemical composition and antioxidant activity of the essential oils of Origanum vulgare subsp. gracile in different plant parts and at different phenological stages. Qualitative and quantitative analyses of the essential oil identified 41 constituents that varied with plant age and organ. The phenolic monoterpenoid carvacrol (18.1–79.2%) was predominant in all the essential oil samples. Other major constituents were p-cymene (3.9–18.0%), γ-terpinene (0.9–15.8%), carvacrol methyl ether (0.8–9.9%), and (Z)-α-bisabolene (0.5–8.7%). Among the different plant parts and phenological growth stages, the highest levels of carvacrol were identified in the essential oils from flowers (79.2%), roots (70%), and the early vegetative growth (67.34%). All the essential oils exhibited high radical-scavenging properties as shown in the DPPH* assay. The essential oils from flowers, however, exhibited the highest antioxidant activity and could be used as a preservative agent on an industrial scale.