Point prevalence surveys of healthcare-associated infections (HAI) and antimicrobial use in the European Union and European Economic Area (EU/EEA) from 2016 to 2017 included 310,755 patients from 1,209 acute care hospitals (ACH) in 28 countries and 117,138 residents from 2,221 long-term care facilities (LTCF) in 23 countries. After national validation, we estimated that 6.5% (cumulative 95% confidence interval (cCI): 5.4–7.8%) patients in ACH and 3.9% (95% cCI: 2.4–6.0%) residents in LTCF had at least one HAI (country-weighted prevalence). On any given day, 98,166 patients (95% cCI: 81,022–117,484) in ACH and 129,940 (95% cCI: 79,570–197,625) residents in LTCF had an HAI. HAI episodes per year were estimated at 8.9 million (95% cCI: 4.6–15.6 million), including 4.5 million (95% cCI: 2.6–7.6 million) in ACH and 4.4 million (95% cCI: 2.0–8.0 million) in LTCF; 3.8 million (95% cCI: 3.1–4.5 million) patients acquired an HAI each year in ACH. Antimicrobial resistance (AMR) to selected AMR markers was 31.6% in ACH and 28.0% in LTCF. Our study confirmed a high annual number of HAI in healthcare facilities in the EU/EEA and indicated that AMR in HAI in LTCF may have reached the same level as in ACH.