BACKGROUND: By 2017, more than 500,000 Syrian refugees had passed through Greece seeking safety and asylum. Understanding how their health needs evolved over the refugee crisis in Greece and in relation to changing migration policy, and exploring the challenges involved in delivering their healthcare is timely as non-governmental organizations (NGOs) transition health service provision to the Greek health authorities. METHODS: We conducted a qualitative study to explore stakeholders' perspectives on delivering health services to Syrian refugees over the course of the humanitarian response in Greece from 2015 to 2017. Twenty-five in-depth interviews were conducted face-to-face or by Skype with healthcare providers, NGO staff, and organizational and government representatives involved in coordinating and managing healthcare for the Syrian refugee population in Greece. Following informed consent, interviews were audio-recorded or detailed summaries were manually recorded. Data were coded inductively to identify emerging themes. RESULTS: Following the implementation of the European Union-Turkey agreement in 2016, healthcare providers in refugee camps reported a shift from acute physical health issues to mental health disorders, and heightened risks of gender-based violence among Syrian refugees. Key challenges to service delivery included a narrow model of healthcare provision and insufficient referral mechanisms for social support and mental health services. Language and gender differences between refugees and healthcare providers, and a lack of privacy and space in clinics impeded the quality of care. Stakeholders observed deterioration in refugees' mental health in relation to longer periods spent in the camps. Many also emphasized that services for gender-based violence and mental health should be prioritized. CONCLUSION: This study provides stakeholders' perspectives on changes in refugee health needs over the course of the humanitarian response in Greece. With protracted encampment resulting from migration policy, addressing mental health disorders and gender-based violence should be prioritized, including psychosocial training for healthcare providers and strengthening referral mechanisms for specialized care. The findings also emphasize the importance of providing human-centered care and gender concordant services by incorporating female healthcare providers and interpreters into medical teams. Strategic communication and coordination is needed between NGOs and Greek health authorities to facilitate the transition of health service delivery to the Greek healthcare system and to improve access and quality of care for refugees.