Acanthamoeba species are free-living amoebae that constitute an etiological agent of Acanthamoeba keratitis, an illness that may cause severe ocular inflammation and blindness and has a very difficult treatment. These molecules that are found in plants may be an alternative for the development of new drugs. Plants of the genus Pterocaulon (Asteraceae) are used in folk medicine as an antiseptic and antifungal agent. In this work, we analyzed Pterocaulon polystachyum essential oil and assessed its amoebicidal activity against Acanthamoeba polyphaga. The leaves of the fresh plant submitted to hydrodistillation yielded 0.15% (w/v) of essential oil that was analyzed by gas chromatography-mass spectrometry being E-sesquilavandulyl acetate as the major component, representing 43.8% of the oil. For the assessment of the amoebicidal activity, concentrations of 20, 10, 5, 2.5, and 1.25 mg/mL of essential oil were tested, being lethal to 100% of the A. polyphaga trophozoites at the concentrations of 10 and 20 mg/mL in 24 and 48 h. The cytotoxic effect of essential oil was also tested in mammalian cells using MTT assay. Amoebicidal activity results are in accordance with previous work in which the lipophilic compounds from this plant were active against Acanthamoeba castellanii. However, further studies with the major component of the essential oil will be carried out.