In modern organizations specific software is widely used. This fact is the background for one of the most urgent issues in the activity of any organization: whether currently used software complies with the terms of license agreement. In many companies the set of licenses bought for the use of software doesn't not correlate to actual installations on users' computers. This is the very reason why companies are not protected from possible discrepancy of bought and installed licenses, in spite of considerable budget investments. Such a discrepancy causes financial, legal and other risks. This study reveals the deficiencies of available approaches to the construction of license management system. It contains method guides developed for removal of identified deficiencies in the available approaches to the construction of license management systems. Integrated innovative system of management and accounting of licenses was developed, which corresponds to all methodological recommendations, developed on the previous stage. This system makes it possible to build transparent interrelations between software installed in the company and bought license for the use of software under consideration, which gives us the opportunity to observe strictly intellectual property law. The developed system has been implemented and frequently used in a large Russian company since June 2016 by this day. The article shows the results of exploitation period and confirms consistency of the developed system as the management tool of the licenses for the use of software.