In this study, we extracted the essential oils of the stem, leaf, and flower of Achillea filipendulina, analyzed them, and studied their antibacterial properties. Of 16, 53, and 35 compounds identified in the stem, leaf, and flowers, respectively, only five are present in all three segments of the plant. The essential oil of the stem was mainly composed of neryl acetate, spathulenol, carvacrol, santolina alcohol, and trans-caryophyllene oxide. However, the main identified components of leaf were 1,8-cineole, camphor, ascaridole, trans-isoascaridole, and piperitone oxide and the main components of the flower oil were ascaridole, trans-isoascaridole, 1,8-cineole, p-cymene, and camphor. The extracted oil from different segments demonstrated varying antibacterial properties against both Gram-positive and Gram-negative bacteria, demonstrated by disk, minimum inhibitory concentration, and minimum bactericidal concentration methods. These suggest that the application of all segments of aerial parts of A. filipendulina may have a better therapeutic effect in fighting pathogenic systems.