Decision making can be a complicated process, especially when we need to consider a large number of factors. In the case of companies implementing Lean Manufacturing, the vast variety of lean tools makes it harder to select the right tools for the right system at the right time. In this paper, a systematic approach is proposed to assist the decision making process in two steps. In the first step, a Gap Analysis is carried out to compare the current state of the system with a benchmark to identify the deficiency of performance in various categories. The second step employs the Analytic Network Process (ANP) to prioritize lean tools by evaluating the needs and urgency of improvements. We use ANP to prioritize a list of lean tools that need to be implemented urgently considering the current status of a manufacturing firm. A hypothetical case study demonstrates that the proposed decision making approach is capable in selecting lean tools that are applicable, suitable, and urgently needed according to user's inputs.