Background: Medicinal plants are the major sources of the crude drugs and natural antioxidants. Berberis species have been used in the treatment of various ailments around the world including Nepal. However, systematic study on phytochemistry and pharmacology of Berberis species from Nepal is lacking. Objectives: To evaluate the antioxidant activity, total phenolic and flavonoid contents of Berberis aristata and Berberis thomsoniana from Sagarmatha National Park. Materials and Methods: Antioxidant activity was measured through 2, 2-Diphenyl-1-Picrylhydrazyl assay. Total phenolic and flavonoid content were estimated using Folin–Ciocalteau and aluminum chloride method respectively. Results: Samples showed dose-dependent radical scavenging activity. Radical scavenging activity of the methanolic extracts of different parts of B. aristata and B. thomsoniana ranged from 19.38 to 98.47%, with leaf extracts of B. thomsoniana showing the strongest activity. The total phenolic content of the samples varied from 11.04 to 65.30 mg GAE g-1 dry weight whereas total flavonoid content was in between 2.4 to 16.46 mg quercetin/g dry weight. Conclusion: Among the tested samples, leaf extracts of B. thomsoniana showed the strongest antioxidant activity and contained the highest amount of total phenolic and flavonoid content.