Psychosocial stress and pain may relate to educational selection. At the end of primary school (International Standard Classification of Education: ISCED level 1) children are recommended for one of three performance-based lower secondary level types of school (ISCED level 2). The study examines the association of educational selection and other risk factors with pain in the upper back (UBP), lower back pain (LBP), peripheral (limb) pain (PP), and abdominal pain (AP). Teacher reports of unsatisfactory grades in mathematics, and official school-type recommendation are included as objective psychosocial risk factors. One hundred and ninety-two schoolchildren, aged between 10 and 13 from 11 classes of 7 schools in Switzerland participated in the cross-sectional study. In logistic regression analysis, predictor variables included age, sex, BMI, participation in sport, physical mobility, weight of satchel, hours of daily TV, video, and computer use, pupils' back pain reported by the mother and father, psychosocial strain, unsatisfactory grade in mathematics, and school-type recommendation. Analysis of pain drawings was highly reliable and revealed high prevalence rates of musculoskeletal pain in the last 4 weeks (UBP 15.3%, LBP 13:8%, PP 33.9%, AP 20.1%). Psychosocial risk factors were uniquely significant predictors of UBP (psychosocial strain), LBP (psychosocial strain, unsatisfactory grade in mathematics, school-type recommendation), and AP (school-type recommendation). In conclusion, selection in terms of educational school system was uniquely associated with LBP in schoolchildren. Stress caused by educational selection should be addressed in primary prevention of musculoskeletal pain in schoolchildren.