Essential oils from plants used in traditional medicine are known as a rich source of chemically diverse compounds with specific biological activities. Achillea millefolium essential oil (AEO) was screened for in vitro activity against Babesia canis. The AEO was obtained by hydrodistillation and analysed by gas chromatography coupled to mass spectrometry (GC-MS). GC-MS revealed the presence of 47 compounds in the essential oil. Those present in the highest concentrations were chamazulene (34.45%), β-caryophyllene (8.93%), (E)-germacrene D (7.55%), patchoulene (7.27%), β-guaiene (4.62%), α-humulene (4.59%), santolina epoxide (4.41%), ethyl iso-allocholate (2.97%), aromadendrene (2.62%), and neoclovenoxid-alkohol (2.46%). AEO was found to be active in vitro against B. canis, with 50% inhibitory concentration (IC50) values of 0.06 mg/mL, as compared to imidocarb, with IC50 = 0.007 mg/mL. The study confirms that essential oil from A. millefolium has anti-babesial properties in vitro.