Intellectual capital occupies a significant place among factors of economic development of such regional formations as sciencecities of the Russian Federation. In the paper there is formulated the author’s definition of intellectual capital of a territory as a category providing income growth both of single man and a science city as a whole and being a source and a basis for economy innovation development. To achieve management purposes, in authors’ opinion, the concept of an “intellectual capital level” (ICL) is more suitable which combines intellectual capital and the results of its realization. The identification of factors in management effectiveness is carried out with the use of characteristics in population life quality and the correspondence of scientific-industrial-complex indices of a municipal region to the science city status of the Russian Federation. The decomposition-aggregate method offered for the ICL assessment allows defining efficiently the ICL of a science city revealing problem areas managing in a system way an intellectual capital level increasing a living standard of population and keeping a high status of a ”science city of the RF”.