Agastache rugosa (Fisch. & C. A. Mey.) Kuntze known as Korean Mint is a medicinal and aromatic plant containing rosmarinic acid as a major bioactive polyphenol but its content in this herbal drug is variable. Plant in vitro culture is one of the approaches used to overcome the complexity of environmental factors influencing phytochemical profiles in medicinal plants. In this study, hairy root cultures of A. rugosa were established through the infection of Rhizobium rhizogenes. Four hairy roots lines were selected on the basis of biomass production in liquid media. Transformation was confirmed by PCR using rol C specific primers. The hairy roots were successfully cultured in 300 mL conical flasks and scaled-up using three bioreactor types (nutrient sprinkle bioreactor—NSB and two modular temporary immersion systems—RITA® and Plantform®). The UPLC analysis of A. rugosa transformed roots methanol extracts showed the presence of 24 polyphenolic compounds with the predominance of rosmarinic acid (RA), which level ranged between 3.82 and 9.16 mg/g of dry weight, depending on the culture system. Nineteen compounds were identified in hairy roots growing in NSB system, 9 of them were identified in roots cultured in RITA® or Plantform® and 7 compounds were identified in roots from Erlenmeyer flasks. The R. rhizogenes infection (strain A4) was found to be an effective method of hairy root culture establishment of A. rugosa.