We propose methods for competitively optimizing state funding of higher education institutions and scientific institutions based on the use of information technologies. These organizations are financed, not the results of their activities. Optimization for scientific institutions is carried out based on indicators of the effectiveness of their scientific activity. The optimization of higher education institutions additionally includes indicators of the effectiveness of graduate training. Methods have also been developed for cleaning indicators of scientific activity from deception. Application of the obtained results will allow the Government of Ukraine to make decisions based on a system of objective indicators for the contribution to the international science and the country’s economy made by higher education and scientific institutions. The specific choice of motivational conditions is a decision of the Government of Ukraine, which will have the opportunity to rely on objective indicators and characteristics.