Abstract Background An estimated 1,174,140 refugees have migrated into Greece, a main entry point for refugees into Europe, since 2014. Their infectious disease profile is monitored by a national-level ad-hoc syndromic surveillance system in refugee-migrant reception centres. The utility of this system is explored to contribute evidence to and improve syndromic surveillance in European refugee responses. Methods Proportional morbidities, numbers of cases and signals, cases above expected numbers, of 14 syndromes are collated from weekly reports between 2016-2019, graphed and analysed in the context of the humanitarian response. Semi-structured key informant interviews are conducted and thematically analysed. Results Between 20.06.2016 and 17.02.2019, 36358 cases and 116 signals occurred. Public health responses resulted and there were no significant outbreaks. On average 5% of all consultations in centres were on infectious syndromes. Respiratory infections with fever (57%), gastroenteritis (22%), suspected scabies (13%) and rashes with fever (5%) were most commonly reported. Every week, between 68-100% of 25-58 participating centres completed reporting adequately. 6 informants reported on their syndromic system user experience. The system’s benefits, providing information and safeguarding refugees, outweighed harms. Data was timely and complete, but likely under-reported for common conditions. Poor living conditions and inter-agency coordination complicated reporting and public health responses. Conclusions Infectious burdens and trends were provided by the system and allowed for timely responses. Data quality was adequate. The system was valuable and feasible to informants. The set-up of the humanitarian response, inadequate ownership and poor coordination of authorities reduced the system’s utility. Key messages Syndromic surveillance is useful for monitoring refugee infectious health. Structural barriers need to be resolved to improve systems’ data and user experience.