Strategic lean management (LM) efforts almost always fail because Leaders often lack a map of their own organization. The reason for this might be that scholars have so far mostly provided qualitative or rigid one-size-fits-all frameworks for strategically designing organizations. The purpose of this paper is to provide a comprehensive quantifiable framework for strategically designing organizations for LM. Combining knowledge about strategic organizational design (SOD) and LM, we introduce a novel theory called “Lean Brain Theory” (LBT). LBT considers organizations as networks with organizational structure, functional connectivity and effective dynamic patterns in the quest of attaining an optimal SOD towards the strategic goal of LM. To reinforce the new paradigm, the analogy between a Lean organization and a human brain is depicted. The future of Lean organizations relies on strategically designing its structure, function and effective dynamics so as to emulate the Human Brain.