Health benefits packages (HBPs) are increasingly used in many countries to guide spending priorities on the path towards universal health coverage. Their design is, however, informed by an uncertain evidence base but research funds available to address this are limited. This gives rise to the question of which piece of research relating to the cost-effectiveness of interventions would most contribute to improving resource allocation. We propose to incorporate research prioritisation as an integral part of HBP design. We have, therefore, developed a framework and a freely available companion stand-alone tool, to quantify in terms of net disability-adjusted life-years (DALYs) averted, the value of research for the interventions considered for inclusion in a package. Using the tool, the framework can be implemented using sensitivity analysis results typically reported in cost-effectiveness studies. To illustrate the framework, we applied the tool to the evidence base that informed the Malawi Health Sector Strategic Plan 2017-2022. Out of 21 interventions considered, 8 investment decisions were found to be uncertain and three showed strong potential for research to generate large health gains: 'male circumcision', 'community-management of acute malnutrition in children' and 'isoniazid preventive therapy in HIV +individuals', with a potential to avert up to 65 762, 36 438 and 20 132 net DALYs, respectively. Our work can help set research priorities in resource-constrained settings so that research funds are invested where they have the largest potential to impact on the population health generated via HBPs.