Enterprise optimization has become a major target in the pharmaceutical industry because of the increasing pressure for staying relevant in the worldwide commercial center. The ever-increasing competition, changing regulatory requirements, new emerging technologies along with a lot of other factors are pushing pharmaceutical manufacturers towards Enterprise optimization for the purpose of fast-Tracking innovation to boost their productivity and product quality. The objectives of Enterprise optimization include profit maximization, asset utilization, management of inventory levels, and coordinated decision making. These business exercises are moderately troublesome because of the association of various risk factors. In this paper, applications that have relevance to Enterprise optimization have been reviewed, with special attention to innovative drug development life cycles which are prone to substantial risks. This paper proposes a decision-making methodology with the identification of uncertainties and risks based on the Fuzzy AHP approach. © 2021 IEEE.