Child injuries are a major public health concern worldwide. Estimates on child injuries are scarce in the Eastern Mediterranean Region (EMR). We assessed the prevalence of injuries amongst secondary school students in the EMR. We analyzed secondary data from the Global School Health Surveys (GSHS) from 17 EMR countries. It is a multi-stage and school-based survey that collects information on risky behaviors including injuries among 11–16 year old school students. Study variables included demographic characteristics, number of injuries, type and frequency of injuries in the past 12 months. Forty percent of students reported being seriously injured at least once in the past 12 months. These injuries were largely attributed to road traffic crashes (18%) and falls (10%). Majority of the injury types were cuts or stabs (7%) and broken bones or dislocated joints (5%). However, a significant proportion of the students failed to elaborate their injury and indicated their injury to be of ‘something else’ (8%). 23% of these unknown types of injuries were also caused by someone trying to hurt them by purpose. More than one third of school students in the EMR were seriously injured at least once during the past 12 months. There is a need to understand the injury category defined as ‘something else’ as this category could have been caused by something the child might not want to speak of but be of serious consequences. Otherwise, health agencies, schools and governments will not be able to intervene appropriately and implement the adequate youth injury prevention programs.