In extremely dynamic and volatile environment contemporary companies have to rapidly adapt to external conditions and become highly flexible. In such environment common task of management and controlling is to keep vitality and to achieve competitive advantage and business success. Controlling, as management's expert support, ensures transparency and applying of methods to accomplish effectiveness and efficiency in management work. Business intelligence, as a fundamental of intelligent companies, in last few decades evolved through several complementary phases, based on strong technological development. Evolution of controlling has been tightly connected to applying information technology. With appearance of business intelligence and deployment in business, controlling has got one of the most important data sources in information flow, on strategic, tactical and operational level. From above mentioned facts derive the basic objectives of this paper: to explore and point to controlling role on operational and strategic level, in applying and upgrade of business intelligence in company, challenges in which it encounters, and improvement possibilities. The key factor of success is collaboration and balance of business and IT. The role of controlling is, by means of coordination and integration principles, to contribute to successful appliance of business intelligence in company, thereby increasing effectiveness and efficiency.