This study aimed to investigate the various biological activities of Geranium thunbergii such as antimicrobial activity and protective effect against oxidative damage. To evaluate its antioxidant and antimicrobial activities, we first performed methanol extraction; this methanol extract was further partitioned using various solvents. And then, its antioxidant activity was measured using various assays including total phenolic content and protection against oxidative DNA damage, and antimicrobial activities were examined using minimum inhibiting concentration (MIC) test, and paper disc method. In addition, high-performance liquid chromatography was performed to analyze the major chemical components of ethyl acetate fraction. The G. thunbergii fraction with ethyl acetate exhibited higher antioxidant and antimicrobial activities than the other fractions. The results showed that G. thunbergii ethyl acetate fraction at 50 μg/mL had strong DPPH and ABTS radical scavenging activities of 80.88% and 80.12%, respectively. In addition, the ethyl acetate fraction protected DNA from the oxidative damage induced by ferrous ion and hydroxyl radicals and showed high antimicrobial activity with diameter of inhibition zones ranging from 13.33 to 15.67 mm. High-performance liquid chromatography analysis revealed the major phenolic compounds of G. thunbergii to be ellagic acid and gallic acid. These results suggest that G. thunbergii might protect DNA against oxidative stress induced by reactive oxygen species and can be utilized as a natural source of antioxidant and antimicrobial agent in the food industry.