Background: Palestine, like other low-income countries, is confronting an increasing epidemic of non-communicable disease (NCD) and trend of war injury. The management of health problems often presents a critical challenge to the Palestinian health system (PHS). Understanding the perceptions of healthcare providers is essential in exploring the gaps in the health system to develop an effective healthcare intervention. Unfortunately, health research on management of NCD and war injury has largely been neglected and received little attention. Therefore, the study aimed to explore the perspectives of healthcare providers regarding NCD and war injury management in the PHS in the Gaza Strip. Methods: A qualitative study approach was used, based on four focus group discussions (FGDs) involving a purposive sampling strategy of 30 healthcare providers from three main public hospitals in Gaza Strip. A semi-structured topic guide was used, and the focus group interviews data were analyzed using manifest content analysis. The study was approved by the Palestinian Health Research Council (PHRC) for ethics approval. Results: From the healthcare providers perspective, four main themes and several subthemes have emerged from the descriptive manifest content analysis: functioning of healthcare system; system-related challenges; patients-related challenges; strategies and actions to navigating the challenges and improving care. Informants frequently discussed that despite some positive aspects in the system, fundamental changes and significant improvements are needed. Some expressed serious concerns that the healthcare system needs complete rebuilding to facilitate the management of NCD and war-related injury. They perceived important barriers to effective management of NCD and war injury such as poor hospital infrastructure and logistics, shortage of micro and sub-specialities and essential resources. Participants also expressed a dilemma and troubles in communication and interactions, especially during emergencies or crises. The informants stressed the unused of updated clinical management guidelines. There was a consensus regarding poor shared-care/task sharing, partnership, and cooperation among healthcare facilities. Conclusion: Our findings suggest that fundamental changes and significant reforms are needed in the health system to make healthcare services more effective, timely, and efficient. The study disclosed the non-use of clinical guidelines as well as suboptimal sectorial tasksharing among different stakeholders and healthcare providers. A clear and comprehensive healthcare policy considering the gaps in the system must be adopted for the improvement and development of care in the PHS.