Plants belonging to the genus Artemisia L. have been used for medicinal purposes since ancient times. These aromatic plants produce and accumulate a wide range of potent secondary metabolites, many of which have shown antioxidant, antiparasitic, antimicrobial, anti-inflammatory, and even anticancer activities. Enhanced biosynthesis of these compounds is a prerequisite for comprehensive studies of their therapeutic properties and cost-efficient use. Transformation of plants with Agrobacterium rhizogenes native root locus (rol) genes is a promising approach to increase the biosynthesis of plant secondary metabolites. The aim of the present study was to evaluate the effects of A. rhizogenes-mediated transformation on the flavonoid contents in hairy roots of medicinal herb A. tilesii Ledeb. Transgenic A. tilesii hairy root lines were analyzed for stable integration of the rolB and rolC transgenes into the plant genome, total flavonoid contents, antioxidant activities of extracts, and the spatiotemporal expression of two flavonoid biosynthetic genes, phenylalanine ammonialyase (PAL) and chalcone synthase (CHS). The flavonoid contents of A. tilesii directly correlated with the antiradical activity and reducing power of their respective lines, with the greatest antioxidant activity found in the plants with the highest level of total flavonoids. Furthermore, all hairy root lines demonstrated altered expression of plant native PAL and CHS genes. Most importantly, A. rhizogenes-mediated transformation enhanced the biosynthesis of natural antioxidants in A. tilesii, producing almost twice the amount of flavonoids than controls. These findings provide an opportunity for the identification of the bioactive molecules in A. tilesii extracts and their potential health benefits.