The total phenolic and flavonoid contents, antioxidant and antibacterial properties of flavonoid- (water, ethyl acetate and hexane fractions), polyphenol- and anthocyanin-rich extracts of Thymus kotschyanus aerial parts were investigated. All the extracts showed significant amounts of phenolic and flavonoid compounds and exhibited strong antioxidant activity. Among the extracts, water fraction contained the highest phenolic and flavonoid contents (881.06 ± 16.52 mg GAE/g of extract and 74.60 ± 3.05 mg QE/g of extract, respectively). It also presented the highest DPPH• scavenging activity with an IC50 of 14.21 ± 0.53 μg mL−1, and the highest reducing power at 400 μg mL−1 by A700 = 2.46 ± 0.04. The extracts were found to exert moderate antibacterial activity against both Gram-negative and Gram-positive bacteria. These findings highlighted a scientific basis to the traditional usage of T. kotschyanus, also showed its potential as a rich source of natural antioxidant and antibacterial compounds.