Performance evaluation plays an important role in determining faults and difficulties of any supply chain as well as attempting to increase capabilities and improve activities. Data envelopment analysis (DEA), as a non-parametric method, has been one of the most important and significant management tools for measuring output or efficiency. In fact, in a real evaluation problem input and output data of entities evaluated often fluctuate. These fluctuating data can be represented as linguistic variables characterized by fuzzy numbers for reflecting a kind of general feeling or experience of experts. Based on the fundamental CCR model, a fuzzy DEA model is proposed to deal with the efficiency evaluation problem with the given fuzzy input and output data.. In this paper, we propose a method to utilize balanced score card (BSC) as a tool for designing performance evaluation indices of an supply chain. The integrated BSC-FDEA has been applied as an empirical case for Iranian dairy industry supply chains and the results are analyzed.