Apart from the severe impact on public health and well-being, the chain effect resulting from the COVID-19 health crisis is a profound disruption for various other sectors, notably in education. COVID-19 has driven massive transformation in many aspects of the educational landscape, particularly as teaching and learning shifted online due to school closure. Despite the many impacts of the health crises on school populations, a systematic review regarding this particular issue has yet to be conducted. This study, therefore, attempts to comprehensively review the impact of health crises on school populations (student, teacher, parent, and school administration). An extensive literature search guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) reporting checklist was performed in two selected databases, namely Web of Science (WoS) and Scopus to identify how this particular topic was previously studied. Exclusion and inclusion criteria were set to ensure that only research papers written in English from the year 2000 to the present (April 2021) were included. From a total of 457 studies screened, only 41 of them were deemed eligible to be included for qualitative synthesis. The findings revealed that the COVID-19 pandemic was the only health crisis discussed when it comes to investigating the impact of health crises on school populations. This study found four notable consequences of health crises on school populations, which are impacts on mental health, teaching and learning, quality of life, and physical health. Among factors associated with the impact of the health crises are; demographic factors, concerns about the pandemic, education-related factors, health-related factors, geographic factors, economic concerns, teaching challenges, and parenting in the pandemic. This study is expected to be a reference for future works in formulating crises mitigation strategies to reduce the impact of health crises on schools by exploring the contexts of the crises.