The National Health Vision of Pakistan 2016-2025 is to provide affordable health services through a resilient and responsive health system for achieving health-related Sustainable Development Goals (SDGs) and universal health coverage (UHC) targets. Through this study, we wanted to identify the research priorities at the national level that would help to provide the necessary evidence for achieving this vision through essential package of health services (EPHS). We followed World Health Organization (WHO) guidance for undertaking research priority-setting exercises and the Child Health and Nutrition Research Initiative (CHNRI) methodology in conducting this national exercise. The proposed research options for the next three to five years were identified in five thematic research areas: communicable diseases; non-communicable diseases (NCDs) and injuries; reproductive, maternal, newborn, child, and adolescent health (RMNCAH); mental health; and health systems and services. We assessed these research options against five priority-setting criteria: feasibility, public health importance, sustainability, equity, and community involvement. Forty-three experts proposed 272 research ideas, which were consolidated into a list of 155 research options and sent back to the experts for scoring. The top 10 research priorities in each of the five research areas were identified based on the weighted research priority scores (wRPS) rankings. Tuberculosis and antimicrobial resistance; NCD screening and prevention; maternal and neonatal mortality; mental health of children, adolescents, and youth; and human resource management were the issues that were most frequently reflected in the list of research priorities. Most research priorities aimed to identify barriers to the implementation of interventions. Through this exercise, we identified the top 50 national health research priorities, which also have a strong correlation with EPHS interventions. To realise the findings of this exercise, funding agencies should establish funding mechanisms to support the undertaking of the identified research priorities, and academic researchers should actually utilise them in future studies. Such activities could hopefully contribute to achieving the national health goals.