OBJECTIVES: To assess the accumulated knowledge of the effects of public health emergencies of international concern on disease control and local health systems, and contribute to a better understanding of their effects on health programs and systems. METHODS: This was a systematic review of published and gray literature (in English, Portuguese, or Spanish). Electronic databases (BVS/LILACS, PubMed, and SciELO) and Google Scholar were searched. Search terms were: COVID-19 OR H1N1 OR Ebola OR Zika OR poliomyelitis AND (outbreaks OR epidemics) AND (public health systems OR public health surveillance). RESULTS: A total of 3 508 studies were retrieved, of which 31 met the inclusion criteria. The studies addressed the effects of the emergencies on: communicable diseases notification systems; malaria, HIV/AIDS, tuberculosis, poliomyelitis, and malaria surveillance, control, and treatment; microcephaly; dengue; and vaccinations. The populations affected by the emergencies experienced reduced health services, which included fewer health visits, failures in the diagnostic chain, decrease in vaccination, and increased incidence or underreporting of notifiable diseases. CONCLUSIONS: Socioeconomic inequity is a determinant of the effects of public health emergencies of international concern within affected populations. The diversion of resources and attention from health authorities disproportionately affects vulnerable populations and can lead, over time, to a weakening of health systems. The analysis of the effects of public health emergencies is important for the development of new protocols that can better respond to future crises.