The necessity of restructuring university budgeting from program-based to performance-based budgeting (PBB) leads many studies to be conducted. Reviewing the literature, we observed that there is no mathematical model including Dual PBB Structure in University. The purpose of this paper is to construct a PBB model for university so that the budget is allocated not only to plans based on their priorities, but also to faculties based on approved student per Capita by the Ministry of Sciences, Researches and Technology. Considering the various criteria in the university system and because of fuzzy and stochastic uncertainties in the problem parameters, two scenarios were analyzed. 1) Crisp Lower Bound Robust Fuzzy PBB (CLB-RFPPB) model 2) Fuzzy Lower Bound Robust Fuzzy PBB (FLB-RFPPB) model. A significant point in Both of them, is to use performance Indicators--calculated based on data envelopment analysis approach (DEA) regarding a basic model of input-oriented CCR— determined the importance coefficient for each educational groups in order to allocateing budget. In addition, the weights of Goals and the priority of each plan were determined using some paired comparison questionnaires completed by experts. The PBBGP model has 5 goals, 1142 constraints and 994 decision variables. The results of models solution- that are presented on two macro and Operational Levels- and simulation of Crisp and two RFPBB models, Demonstrate high level capabilities of RFPBB models in response to the uncertainty in the parameters of problem and also managing the level of decision risk