Lysozyme is a hydrolytic enzyme with potent antibacterial activity; its modification further enhances this effect. The modified enzyme shows an improved usability, thus, providing for wider practical utilization thereof. In the hitherto studies on lysozyme, several lysozyme modification methods have been developed including thermal and thermo-chemical methods. A side effect of this type of modification is partial irreversible enzyme denaturation. It induces the worsening of properties of the modified lysozyme and, as a result of its decreased solubility in the water environment, it reduces the practical application of the produced preparations. The objective of this study was an attempt to increase the functionality of thermally modified enzyme through the elimination of insoluble fraction from the preparation. The fractionation performed in a neutral environment resulted in producing a preparation of a complete solubility and hydrolytic activity of 10 000 U/mg. The highest efficiency of the fractionation process (75 %) was achieved in an acidic environment with the use of a 0.18 % hydrochloric acid.