There is a growing international and regional interest in Health Research Systems (HRSs) in light of a global strategy for HRS stakeholders' (HRSSHs) active involvement. HRSSHs in Palestine have rarely been investigated with regard to uncertainties.; This study aimed to analyse perceptions of HRSSHs in order to understand their roles and involvement, identify gaps, and offer policy solutions for stakeholders' engagement in the Palestinian HRS.; This qualitative study targeted three local Palestinian health sectors, government, academia, and local and international agencies. Data were collected through 52 in-depth interviews (IDIs) and 6 focus group discussions (FGDs) and then analysed using MAXQDA 12 software. Participants and institutions were selected purposively based on a set of criteria and peer review.; The overall HRS stakeholders' roles were unsatisfactory, with low involvement from society, the private sector, local and international sectors. The role of academia and the Ministry of Health is vital but observed moderate in health research while that of international agencies is weak due to conflicting agendas and lack of a guiding body. Most universities have poor representation in public decision-making and scarcity in health research potential and capacity. Interest-power imbalance among stakeholders is reported where political, organizational, and technical shortfalls were indicative of weak roles and low involvement, along with a lack of health research culture, structure, resources, defined roles, and network.; Tackling the inadequate roles, interests' disparity, and poor involvement of HRSSHs is imperative for HRS …