How can uncertain fisheries science be linked with good governance processes, thereby increasing fisheries management legitimacy and effectiveness? Reducing the uncertainties around scientific models has long been perceived as the cure of the fisheries management problem. There is however increasing recognition that uncertainty in the numbers will remain. A lack of transparency with respect to these uncertainties can damage the credibility of science. The EU Commission’s proposal for a reformed Common Fisheries Policy calls for more self-management for the fishing industry by increasing fishers’ involvement in the planning and execution of policies and boosting the role of fishers’ organisations. One way of higher transparency and improved participation is to include stakeholders in the modelling process itself. The JAKFISH project (Judgment And Knowledge in Fisheries Involving StakeHolders) invited fisheries stakeholders to participate in the process of framing the management problem, and to give input and evaluate the scientific models that are used to provide fisheries management advice. JAKFISH investigated various tools to assess and communicate uncer- tainty around fish stock assessments and fisheries management. Here, a synthesis is presented of the participatory work carried out in four European fishery case studies (Western Baltic herring, North Sea Nephrops, Central Baltic Herring and Mediterranean swordfish), focussing on the uncertainty tools used, the stakeholders’ responses to these, and the lessons learnt. It is concluded that participatory modelling has the potential to facilitate and structure discussions between scientists and stakeholders about uncertainties and the quality of the knowledge base. It can also contribute to collective learning, increase legitimacy, and advance scientific understanding. However, when approaching real-life situations, modelling should not be seen as the priority objective. Rather, the crucial step in a science–stakeholder collaboration is the joint problem framing in an open, transparent way.