Employees engaged in mental work have become the most valuable assets of any organization in the 21st century. The satisfaction of those involved in mental work requires the provision of objectivity and transparency in their decision-making. This, in turn, entails the development of scientifically motivated decision making mechanisms and scientific-methodological approaches to evaluate their performance based on innovative technologies. The main goal of this article is in development of the scientific and methodological framework for the establishment of a decision support system to manage the employees engaged in mental work and operating in uncertainty. In this regard, initially, the question of evaluating the activities of scientific workers is examined, its characteristic features are determined, and the fuzzy relation model is proposed as a multi-criterion issue formed in uncertainty. Taking into consideration the hierarchical structure of the criteria that allows evaluating the activities of scientific workers, a phased solution method based on an additive aggregation method is proposed. In accordance with the methodology, a functional scheme of the decision support system to manage the scientific personnel is developed. The working principle of each block and the interaction of the blocks are described. The rules for the employees' management decisions are shown by referring to the knowledge production model. Based on the proposed methodological approach, the implementation phases of the decision support system for the management of the scientific workers of the Institute of Information Technology of ANAS are described. To evaluate the employees' performance, the tools to collect initial information, evaluate the system of criteria, define their importance coefficients and mathematical descriptions are provided. Some results of the system software are presented. The opportunities of the system based on the proposed methodology to support enterprise mangers to make scientifically justified decisions are provided.