Selection of an appropriate set of Information System (IS) projects is a critical business activity which is very helpful to all organizations. In this paper, after describing real IS project selection problem of Iran Ministry of Commerce (MOC), we introduce two Data Envelopment Analysis (DEA) models. Then, we show applicability of introduced models for identifying most efficient IS project from 8 competing projects. Then, in order to provide further insight, results of two introduced models are compared. It is notable that using basic DEA models -CCR and BCC- decision maker is not able to find most efficient Decision Making Unit (DMU) since these models identify some of DMUs as efficient which their efficiency scores equal to 1. As an advantage, the applied models can identify most efficient IS (in constant and variable return to scale situations) by solving only one linear programming (LP). So these models are computationally efficient. It is while using the basic DEA models requires decision maker to solve a LP for each IS.