The migration of healthcare workers from developing countries to more economically developed countries is a long-standing and ongoing trend. Loss of qualified staff due to migration can negatively impact healthcare systems. Understanding factors that drive migration is essential to identifying and managing health system needs. Our study explored factors related to the migration intent of healthcare staff in Kosovo, particularly after the COVID-19 pandemic. We carried out a cross-sectional survey of healthcare workers from public and private institutions. The survey analysed the prevalence of willingness to migrate and whether willingness was affected by the pandemic, and calculated crude and adjusted odds ratios for variables which may influence migration willingness. 14.43% of healthcare workers reported aspiration to migrate, and 23.68% reported an increased chance of migrating after the pandemic. Dissatisfaction with wages and working conditions, higher education and private sector engagement were associated with increased odds of migration willingness. After the pandemic, factors related to interpersonal relationships and state response gave lower odds of migration intent. These findings point to potential factors associated with the migration of healthcare workers, which can help policymakers address gaps in national health system strategy.