Sri Lanka is a resource-poor country in the South-East Asian region with good health indices. Ergonomics of children in educational environments is still novel in the region. An exploration into such issues and dissemination of the scientific evidence will stimulate policy makers in both education and health sector. An important ergonomic issue of the classroom is the seating arrangement. Essential aspects of seating include location of the chair and desk in relation to the blackboard and features of the chair and desk. Musculoskeletal pain is considered to be the most important negative effect due to mismatched ergonomics. A school-based descriptive cross sectional study was carried out in a district of Sri Lanka to ascertain the distribution of selected ergonomic factors related to seating arrangements in the classroom of school-going early adolescents and to assess their relationship to musculoskeletal pain. A sample of 1607 school children of Grade 6,7 and 8 were selected using stratified multi-stage cluster sampling method. There were 52.1% (N=838) females and 47.9% (N=769) males. Many ergonomic aspects related to classroom seating arrangements are not conducive for children. Children were seated with a mean distance of 398.04 cm (SD=132.09) to the blackboard. Nearly 23% of children had to turn more than 45~degrees to see the blackboard. A prevalence of > 80% mismatch was found between body dimensions of children and measurements of furniture. Musculoskeletal pain may have resulted from efforts to maintain stability while seated in incompatible furniture. Nearly 36% children complained of recurrent musculoskeletal pain. Musculoskeletal pain may have resulted from efforts to maintain stability while seated in incompatible furniture. Mismatched seat depth - buttock-popliteal length posed 1.59 times risk recurrent musculoskeletal pain. Despite, children perceived a good chair comfort. Use of backrest lowered the risk of recurrent pain. Results shows that programme planners can utilize such evidence to provide simple ergonomic solutions at national and school level.