The article discusses the methodological basis of creating effective system for intellectual work management at the higher education institution. The study of the intellectual work management is caused by the need of today's complicated socio-economic, organizational and educational systems to obtain reliably reproducible repercussions from future professionals based on scientific approach management. We propose a methodology for intellectual work management, based on the interaction of complex concepts such as intellectual resource, intellectual process, intellectual potential and intellectual capital. The intellectual resource can be considered as a combination of knowledge Technologies and scientific discoveries in the course of research and development (R&D) activities. The intellectual potential ensures a high rate of acquiring new knowledge. Intelligence as a mentality quality promotes adaptation to changes in learning based on the experience, comprehension, and application of knowledge. Intellectual capital of the education institution consists of knowledge, accumulated while implementing educational programs and providing educational services, as well as knowledge structures and intellectual value. We believe that their interpenetration and mutual reinforcement allows solving many fundamental, specific and applies problems of intellectual work management. The study of the students' intellectual work within the described methodological framework of management science, in our opinion, forms a coherent system of representations about the attitude of employers to the intellectual work of future professionals that increases their manageability.