Background & objectives Overuse injury is an important public health issue among children and adolescents, which may affect their overall performance. Therefore, the objective is to determine the prevalence and compare overuse injuries among school-going children in hill and valley, rural and urban areas of Manipur and identify factors contributing to overuse injuries. Methods After obtaining approval from school authorities, a cross-sectional study was conducted in three districts of Manipur namely, Imphal West, Bishnupur, and Ukhrul, among 3,600 schoolchildren in the age group of 7-15 yr. An interview schedule using a pretested questionnaire and a proforma was used for data collection. Descriptive statistics were used, such as mean, SD, percentages, etc. Results In this study, 3,600 students participated; the mean age was 13.37 yr. The overall prevalence of overuse injury was 14.39 per cent, which was the highest in Imphal West (50.19%) and among males (53.09%). The commonest overuse injuries were of lower extremities (44.98%) and were observed to be the highest in Bishnupur (49.59%) and among males (45.45%). Back pain was more prevalent in Ukhrul (37.78%) and among females (31.69%). Among lower extremity injuries, the majority had chondromalacia patellae (29.18%) and shin splint (24.03%), and among the upper extremity injuries, 81.25 per cent had neck and arm pain. Interpretation & conclusions The overall prevalence of overuse injuries was 14.39 per cent, and the highest was in Imphal West. We observed a paradigm shift as the students’ back, neck and arm pain increased. These are important public health concerns that need immediate attention, as well as the development of innovative interventions, including health education and appropriate regulations.