AbstractThe relationship between systems engineering and complex systems governance is not clear, especially given the field of ideas and methodologies supporting complex systems governance are in their early years of evolution. This paper looks to practice, drawing lessons from a case example about the role and application of systems engineering in a major reform program, especially in relation to complex systems governance, seeking to inform the evolution of both theory and practice in how these two fields of ideas work better together. The case study comes from the Australian defence maritime community. This community is transforming its approach to regulating and assuring the management of the seaworthiness of its maritime systems across multiple owners and operators and across their capability life cycles. The paper outlines the situation that created the case for change in the regulatory and management approach; and, examines the complication that caused the then Chief of Navy to change the approach half way through the six‐year transformation period. In making this change, ‘traditional’ systems engineering became less visible, and complex systems governance took precedence while still employing systems engineering principles in the design, build and implementation of the transformation program. The paper then considers three questions: what was the nature of the change, why did the change matter and what lessons do we draw for the relationship between complex systems governance and systems engineering? The authors' answers highlight the traps of not connecting the two fields of ideas. They illustrate the value of the viable systems model (VSM) as an architecture for good governance over the design, build, and implementation of change as well as its ongoing operation and evolution. They go so far as to suggest the lessons will add to the discussion of how the International Council of Systems Engineering (INCOSE) can implement the connections it has made between its vision and the United Nations' Sustainability Development Goals (SDG).