BACKGROUND: The conflict in Syria has required humanitarian agencies to implement primary-level services for non-communicable diseases (NCDs) in Jordan, given the high NCD burden amongst Syrian refugees; and to integrate mental health and psychosocial support into NCD services given their comorbidity and treatment interactions. However, no studies have explored the mental health needs of Syrian NCD patients. This paper aims to examine the interaction between physical and mental health of patients with NCDs at a Médecins Sans Frontières (MSF) clinic in Irbid, Jordan, in the context of social suffering. METHODS: This qualitative study involved sixteen semi-structured interviews with Syrian refugee and Jordanian patients and two focus groups with Syrian refugees attending MSF's NCD services in Irbid, and eighteen semi-structured interviews with MSF clinical, managerial and administrative staff. These were conducted by research staff in August 2017 in Irbid, Amman and via Skype. Thematic analysis was used. RESULTS: Respondents describe immense suffering and clearly perceived the interconnectedness of their physical wellbeing, mental health and social circumstances, in keeping with Kleinman's theory of social suffering. There was a 'disconnect' between staff and patients' perceptions of the potential role of the NCD and mental health service in alleviating this suffering. Possible explanations identified included respondent's low expectations of the ability of the service to impact on the root causes of their suffering, normalisation of distress, the prevailing biomedical view of mental ill-health among national clinicians and patients, and humanitarian actors' own cultural standpoints. CONCLUSION: Syrian and Jordanian NCD patients recognise the psychological dimensions of their illness but may not utilize clinic-based humanitarian mental health and psychosocial support services. Humanitarian agencies must engage with NCD patients to elicit their needs and design culturally relevant services.