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In the presented work, we aimed to investigate the antioxidant and possible neuroprotective capacity of extract of the aerial parts of Hypericum alpestre, found in high altitude Armenian landscape. The neuroprotective activity was evaluated using BV-2 wild type (WT) cells and acyl-CoA oxidase 1 (ACOX1) deficient (Acox1-/-) microglial cell lines. In the chemical-based tests, H. alpestre extract showed high antioxidant activity, which was maintained even after heat treatment at 121 °C for 30 min. MTT test showed that the sub-cytotoxic concentration of investigated extracts for both microglial cell lines was 40 µg/mL. There were no significant changes in catalase activity during all period of treatment in both cell lines, meanwhile, SOD activity increased (up to 30%) in WT cells during the 48 h treatment. Increase of SOD activity (up to 50%) in Acox-/- cells was observed under the 24 h treatment. Significant modulation in activity of palmitoyl-CoA oxidase 1 was noticed only during the 48 h treatment of WT microglial cells. These results evidenced the pro-oxidant activity of the investigated extract. This finding can serve as a basis for further evaluation of plant extracts influence on cancer cell lines.