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The hairy root culture of halophyte Nitraria schoberiwas obtained by transforming seedlings’ primary leaves with a wild strain of Agrobacterium rhizogenes15834 SWISS (transformation frequency was 78.7%). The roots’ transgenic status was confirmed by PCR analysis using rolB-, rolC-, virC-, virD1-specific primers. There was a significant increase in the biosynthesis of flavonoids, hydroxycinnamic acids, pectins, protopectins and saponins in hairy roots as compared to intact plant roots. The сatechin content in ethanol extracts of transformed roots’ exceeded this factor 3.8 times in plant roots, but the compound composition of catechin nature in the latter was more diverse. The high antiviral activity of N. schoberihairy root ethanol extracts against influenza virus subtypes A(H5N1), A(H3N2) was revealed, which manifested itself in the effective inhibition of infectivity both in vitro—in MDCK cell culture—and in vivo increasing survival of mice infected with them.