The aims of this paper are twofold. Firstly, to present a review and critical analysis of the varying forms and functions of Multi-Criteria Analysis presented in the literature, and secondly, drawing from this, to introduce methods and processes by which policy leadership can be introduced into such processes for the appraisal of large-scale transport infrastructure projects to form a policy-led multi-criteria analysis.Following the discussion in the first paper of this Special Issue, ‘Presenting the Case for the Application of Multi-Criteria Analysis to Mega Transport Project Infrastructure Appraisal’, this contribution commences by outlining further the generic features and challenges of multi-criteria analysis approaches to project appraisal whilst emphasizing the difference among various frameworks and attendant processes for such approaches. It also highlights the important role/value of the multi-criteria mapping of stakeholder policies and agendas affecting project decision-making as a means of defining and scoping the boundaries of the project exercise under study and the trade-off decision-spaces for stakeholder dialogues and negotiations in their search to arrive at mutually agreed actions and outcomes. The paper discusses how multi-criteria analysis frameworks can be tailor-designed for particular agencies and stakeholders developed around problems, challenges and issues. This is done in the acknowledgement that such exercises, especially when applied to mega infrastructure project appraisal, typically attract a multiple-institutional response and where ultimately an institutional leader (or partnership of stakeholders) exists/emerges that impose its/their priorities on others. Alternatively, the approach can be tailor-made for specific institutions with its imbedded hierarchy of policies and priorities that frame the stakeholder decision space within which other parties can participate and trade off interests.The first part of the paper highlights the important role of scenarios of policy-making contexts and policy leadership indicating the new risks, uncertainties and opportunities these may offer in multi-criteria analysis exercises, indicating that some/many past processes have been conducted outside of any real reference to such matters. In so doing, such applications have them silently and implicitly adopt scenarios and policy assumptions that are not transparent frequently reflecting, it is alleged, ‘business as usual’ circumstances in contexts when the signs are very much that these trends will not/cannot prevail. The authors contend that without explicit policy leadership there is a danger that certain institutional stakeholder priorities will be imposed over others by the most powerful without adequate dialogue. Understanding that this matters a great deal in contexts when project stakeholder powers shifts occur is very significant. Examples of such circumstances are when national governments become, less or more powerful and economically affluent, when relative legislative and regulation powers become less or more binding and powerful, and when a major private sector investor upon which a project depends goes bankrupt.The second half of the paper builds on these observations to offer a generic multi-criteria analysis framework and attendant processes that imbed policy leadership firmly within multi-stakeholder decision-making (termed Policy-led Multi-criteria Analysis). The framework developed is to be applied to mega transport projects via the use of suitable appraisal criteria in the pursuit of sustainable development goals, which seek to address both quantitative and qualitative dimensions and concerns of multiple stakeholders, with particular emphasis on the processes required to identify and incorporate suitable policy leadership, including feedback between appraisal and policy.