Background: Heavy schoolbag is known to cause health problems for school children. The aim of this study was to determine the effects of carrying heavy schoolbags on the musculoskeletal pain among primary school children of the two subsystems in Yaounde, Cameroon. Methods: A cross-sectional study was carried out in primary schools in Yaounde. A total of 457 school-children (8.2 ± 2.2 years) were included, 202 from the French-speaking subsystem, and 255 from the English-speaking subsystem. Parameters studied included weight, height, and schoolbag weight. A questionnaire was used to collect socio-demographic information and potential musculoskeletal pain in three regions: back, shoulders, and neck. Results: The mean weight of children and their bags was 28.4 ± 8.2 kg and 5.2 ± 2.3 kg respectively. More than 50% of schoolchildren in the two subsystems carried a schoolbag weighing more than 15% of body weight. The back (38%) was the least affected area in comparison to the shoulders (58.6%) and neck (42.4%) (p < 0.001). Carrying heavy bags and walking to school was associated with pain in the back, shoulders, and neck. School-children in the French-speaking subsystem had lower risk (adjusted Odds Ratio 0.438, 95% CI = 0.295-0.651; p < 0.001) to develop a sore neck compared to peers from the English-speaking subsystem. Conclusion: Carrying heavy schoolbags is associated to musculoskeletal pain in schoolchildren. The means moving to and from school is a main risk factor of developing musculoskeletal pain. French-speaking schoolchildren develop less neck pain than English-speaking schoolchildren.