Recent research has highlighted that adaptation tends to focus exclusively on the local and direct impacts of climate change and misses the crucial dimension of transboundary climate risk, which all countries are likely to face, irrespective of their level of development. This paper aims to improve the coverage of transboundary climate risk in case-study research for adaptation. It proposes a protocol to help researchers identify how their case studies can incorporate an analysis of transboundary climate risk, thereby supporting more holistic, effective, and just approaches to adaptation. Existing climate risk assessment frameworks and supporting guidelines have significant strengths but also various challenges when applied to the novel context of transboundary climate risk. This is illustrated with reference to the impact chain framework. Its opportunities pertain to both its flexible form and systems-first focus while its constraints include an analytic emphasis on linear cause–effect relationships (that bely the complexity and uncertainty of systemic risk) and its limited applicability to fragmented governance landscapes (in the absence of an effective consideration of risk ownership). After critically examining the suitability of the impact chain framework, a new protocol is introduced, which builds on principles for managing complex risk and frameworks for assessing risk ownership. The protocol is designed to enable case-study researchers to better identify, assess, and appraise transboundary climate risks, as well as enquire into appropriate risk owners and adaptation options across scales. The paper argues for more innovation in adaptation research to better reflect the complexity and interdependency that characterize today’s world.