Abstract Background Capacity for health economics analysis and research is indispensable for evidence-informed allocations of scarce health resources; however, little is known about the experience and capacity strengthening preferences of academics and practitioners in the Eastern Mediterranean region. This study aimed to assess the needs for strengthening health economics capacity in Jordan, Lebanon, the occupied Palestinian territories and Turkey as part of the Research for Health in Conflict in the Middle East and North Africa (R4HC) project. Methods We combined a bibliometric analysis of health economics outputs based on a literature search conducted across seven databases with an online survey of academic researchers and non-academic practitioners. The records included in the bibliometric analysis were original studies and reviews with an explicit economic outcome related to health, disease or disability, had at least one author in Jordan, Lebanon, Palestine or Turkey, and were published between January 2014 and December 2018. Two types of analyses were conducted using VOSviewer software, namely keyword co-occurrence and co-publication networks across countries and organisations. The online survey asked academic researchers, analysts and decision-makers – identified through the bibliometric analysis and regional professional networks – about previous exposure to and priorities for capacity development in health economics. Results Of 15,185 records returned by the literature search, 566 were included in the bibliometric analysis. Organisations in Turkey contributed more than 80% of records and had the broadest and most diverse network of collaborators, nationally and internationally. Only 1% (n = 7) of studies were collaborations between researchers in two or more different jurisdictions. Cost analysis, cost-effectiveness analysis and health system economics were the main health economics topics across the included studies. Economic evaluations, measuring the economic burden of disease and health equity, were reported by survey respondents (n = 80) as the most important areas to develop in. Short courses, learn-by-doing and mentoring from an experienced professional were, in aggregate, the most preferred learning styles. Conclusions Existing pockets of health economic expertise in the region can constitute the base of future capacity development efforts. Building confidence toward applying specific methods and trust toward stimulating cross-jurisdiction collaborations appear essential components for sustainably developing health economics capacity.