The present article describes some characteristics of the effect of essential oil (EO) extracted from <em>Ziziphora clinopodioides</em> harvested from Armenian highlands on microglial cell lines (BV-2 wild-type (WT) and acyl-CoA oxidase1 (ACOX1)-deficient (<em>Acox1</em><sup>–/–</sup>) cells). The mutant cell line was used as a model to investigate cellular oxidative damage following EO treatment. The main components of the tested EO were pulegone, isomenthone, 1,8-cineole, piperitone, and neomenthole, with concentrations of 42.1%, 9.7%, 8.22%, 7.35%, and 5.9%, respectively, in plants harvested from the high-altitude Armenian landscape. The IC<sub>50</sub> value of the EO in the DPPH assay was 7.025 µL/mL. The sub-cytotoxic concentrations (based on the MTT assay) for both cell lines were 5 × 10<sup>–1 </sup>µL/mL. The catalase activity of the WT cells was decreased following 24-h treatment with the EO, but that of <em>Acox1<sup>–/</sup></em><sup>–</sup> BV-2 cellswas increased. ACOX1 activity was decreased (up to 49%) at 72hof treatment. These results show the protective effect of the tested EO on Acox1<sup>–/–</sup> mutantcells.