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Background Migrants' access to healthcare services is limited. This study aimed to identify health system barriers to vaccination, specifically HPV/MMR vaccination among children in Ukrainian economic migrants (UMs). Methods Between December 2021-March 2022, a qualitative study of UMs living in Poland was conducted. Six focus groups were held with 53 UMs aged 15-45; in-depth interviews with 12 healthcare workers (HCWs) were also performed. A thematic analysis was conducted based on the six WHO health system building blocks. Results HCWs described gaps in integrating migrant status in accessible healthcare data which impeded active management of vaccination procedures. UMs reported that the digitization of healthcare services, intensified during the COVID-19 pandemic, reduced their access to primary care. Inadequate health information systems caused problems with the provision of credible vaccine information in translated forms, and language difficulties, experienced by both UMs and HCWs; this was enhanced by a lack of professional interpreting services. Although most UMs reported vaccinating children according to the Polish schedule, the variations in schedules across countries caused concern among UMs and increased HCWs' uncertainty about how to interpret vaccination cards, particularly in the context of possible false certificates. UMs were affected by discrimination through HCWs. HPV was deprioritized by UMs due to misconceptions about non-mandatory vaccinations; the cost was also a barrier. Conclusions The study findings have implications for migrant vaccination delivery targeting children in Poland, and other UMs receiving countries. A concerted effort is required to improve UM's awareness of the significance of vaccinations. Barriers to healthcare access must be recognized by policymakers. Importantly, removing the cost barrier may increase the uptake of the HPV vaccine among Ukrainian migrant adolescents.