Background The Safety Case is a regulatory technique that requires organisations to demonstrate to regulators that they have systematically identified hazards in their systems and reduced risks to being as low as reasonably practicable. It is used in several high-risk sectors, but only in a very limited way in healthcare. We examined the first documented attempt to apply the Safety Case methodology to clinical pathways. Methods Data are drawn from a mixed-methods evaluation of the Safer Clinical Systems programme. The development of a Safety Case for a defined clinical pathway was a centrepiece of the programme. We base our analysis on 143 interviews covering all aspects of the programme and on analysis of 13 Safety Cases produced by clinical teams. Results The principles behind a proactive, systematic approach to identifying and controlling risk that could be curated in a single document were broadly welcomed by participants, but was not straightforward to deliver. Compiling Safety Cases helped teams to identify safety hazards in clinical pathways, some of which had been previously occluded. However, the work of compiling Safety Cases was demanding of scarce skill and resource. Not all problems identified through proactive methods were tractable to the efforts of front-line staff. Some persistent hazards, originating from institutional and organisational vulnerabilities, appeared also to be out of the scope of control of even the board level of organisations. A particular dilemma for organisational senior leadership was whether to prioritise fixing the risks proactively identified in Safety Cases over other pressing issues, including those that had already resulted in harm. Conclusions The Safety Case approach was recognised by those involved in the Safer Clinical Systems programme as having potential value. However, it is also fraught with challenge, highlighting the limitations of efforts to transfer safety management practices to healthcare from other sectors.