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The optimal allocation of limited resources along with output target setting are critical in pursuing the sustainability and competitiveness of organizations. The process of resource distribution is usually implemented through a central unit that routes resources to the subordinate decision-making units (DMUs) along with DMUs lower bounds of desired efficiency. Moreover, the central unit has the authority to set the overall expected output targets so as to maximize organizational effectiveness. In this paper, we tackle evaluation efficiency questions using a type of bilevel network data envelopment analysis (DEA) approach within a stochastic framework. The proposed bilevel DEA model takes into account stochastic conditions and optimizes centralized resource allocation and target setting, imposing lower bounds on the efficiencies of all DMUs affiliated to the organization. Consequently, the total input consumption is minimized, and the total output production is maximized while considering additional bounds and availability constraints for inputs. In the proposed bilevel model, uncertainty is introduced through the upper level (leader) problem that attempts to maximize organizational effectiveness, while in the lower level (follower) problem, the efficiency of the subordinate DMUs is evaluated. A solution methodology for the bilevel network DEA-based model is presented and numerical results are obtained using data from the literature. The obtained results are compared with those published in other case studies for centralized resource allocation DEA models. [ABSTRACT FROM AUTHOR]