Background: The preliminary experiments indicated that a 30% aqueous extract of seeds of the Terminalia chebula has a significant neutralizing activity against tick-borne encephalitis virus (TBEV). In this study, we developed the most gentle approach to purify the antiviral substance. Methods and Results: The extract of T. chebula seeds was fractionated using gel filtration in Sephadex G-200 and G-50. The fractions were tested in vitro for the presence of a direct antiviral action against TBEV and profiled using liquid chromatographymass spectrometry (LC-MS). Antiviral activity was detected in eight fractions from Sephadex G-200 and in three fractions from Sephadex G-50 gel filtration. The chromatogram of the most active Sephadex G-50 fraction exhibited three base peaks with a retention time of 3, 5 and 25.5 minutes. The MS of individual peaks revealed seven compounds with mass-to-charge ratios 114.03; 279.16; 290.91; 301.15; 579.3; 354.03, and 414.09 that were present at relatively high concentrations. Conclusion: In spite of a small sample, it was possible to detect antiviral activity in the fractionated plant extract using convenient virological methods, as well as to separate the components of the single virus-neutralizing fraction using the LC-MS approach. The purity of resulting preparation needs to be improved.