Background: The World Health Organization (WHO) proposed a global strategy to build a robust Health Research System Resources and Infrastructural Capacity (HRSRIC). Despite the growing research productivity, HRSRIC in Palestine has rarely been investigated. Aims: This study aims to analyse perceptions of health research system performers in order to understand the status of HRSRIC, to identify its gaps, and to propose policy solutions to strengthen the HRSRIC. Methods: This qualitative study targeted three health sectors, government, academia, and local and international organizations. Fifty-two in-depth interviews (IDIs) and 6 focus group discussions (FGDs) were conducted with key-informants who were selected purposively. Data were analysed by using MAXQDA 12. Results: Despite the availability of competent personnel, the overall HRSRIC such as human and financial resources, and facilities form a central challenge. Health research (HR) financing is limited, unsustainable, and flows from external and individual sources. The public and private funds are largely in shortage with resources misallocation and donors' conditionality. HR quality is moderate while knowledge transfer and translation are not well-conceptualized and inappropriately performed. Lack of governance, coordination, HRSRIC strategy, resource allocation, systematic and reliable data, evidence-informed culture, and environmental impacts are the main common gaps. Conclusions: The overall status of HRSRIC in Palestine is still lacking and major challenges persist where the pace of strengthening efforts is steady. There is an emphasis that strengthening HRSRIC is an imperative step and real investment opportunity for building a successful HRS. Political commitment, consolidated leadership structure, operational capacity building-strengthening strategy, and resources mobilization and sovereignty are key requirements.