Objectives To investigate the epidemiological characteristics of the public health emergencies at schools in the Inner Mongolia Autonomous region in 2012-2016, and to provide scientific bases for efficient prevention and treatment.

Methods Descriptive epidemiological method was used to analyze the public health emergencies at schools reported in Inner Mongolia in the past 5 years.

Results In total of 48 public health emergencies at schools were reported during 2012-2016. There were no major or extraordinarily major public events. There were 1 larger level event (2.08%), 42 general level events (87.50%) and 5 unclassified events (10.42%). Emergency category was dominated by respiratory infectious diseases with a total of 26 events, accounting for 54.16% of total school emergencies. The disease category was dominated by mumps and varicella, accounting for 45.83% of the total school emergencies, followed by 10 intestinal infectious disease events dominated by hand foot mouth disease, accounting for 20.83% of total school emergencies. There were two high incidence periods, from March to June and from September to December every year, with the number of events occurred accounted for 58.33% and 41.67% of all emergencies, respectively. Primary schools were the major places of public health emergencies with higher incidence, accounting for 45.83%.

Conclusions Primary schools were the major places of public health emergencies with higher incidence, especially the primary schools in county and town areas. It is necessary to attract attention from administrations of education and health, and actively take effective measures on prevention and control as well as coping strategies.