Information Technology is recognized as a competitive enabler in today’s dynamic business environment. Therefore, alliance of business and Information Technology process is critical, which is mostly emphasized in Information Technology governance frameworks. On the other hand, Enterprise Architectures are deployed to steer organizations for achieving their objectives while being responsive to changes. Thus, it is proposed to align the business and Information Technology through investigating the suitability of Enterprise Architecture scenarios. In view of this fact, investigating a flexible decision making method for business and information technology alignment analysis is necessary, but it is not sufficient since the subjective analysis is always perturbed by some degree of uncertainty. Therefore, we have developed a new robust Data Envelopment Analysis technique designed for Enterprise Architecture scenario analysis. Several numerical experiments and a sensitivity analysis are designed to show the performance, significance, and flexibility of the proposed method in a real case.