The A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences has developed an original active pharmaceutical ingredient based on an oxidized cyclodextrin oligosaccharide, which is a bisulfite derivative. Conducted pharmacological studies proved its antiviral activity in vitro and in vivo experiments against the influenza A (H1N1) virus. The aim of this work was to optimize the technology of obtaining the active pharmaceutical ingredient based on the bisulfite derivative of oxidized cyclodextrin to increase the efficiency and safety of the process. For this, a scaled method of oligosaccharide oxidation was tested on pilot plants in accordance with the requirements of green chemistry. As a result, the reaction time was reduced from three to five days (laboratory conditions) to 1.5 h, and the safety and environmental friendliness of process was ensured. The use of cross-flow filtration and the method of freeze-drying eliminated 96% of ethyl alcohol, reduced the laboriousness and energy consumption of the technological operations for purification and isolation of the final product, and also increased the productivity of the whole process (output increased to 98%). The results are confirmed by data obtained by physicochemical methods.