Musculoskeletal discomfort in schoolchildren is significantly related to the weight and mode of carrying backpack to school. Prevalence and patterns of musculoskeletal discomfort among Nigerian secondary school students carrying backpack was investigated. Systematic sampling technique was used in the selection of the participating junior secondary schools for this study. Participants comprised 1,785 students aged 10-15 years. Standardised Nordic musculoskeletal questionnaire was used to collect information on musculoskeletal pain. Backpack weight and participants' body weight were measured using a weighing scale. The visual analogue scale was used to assess pain intensity. Gender differences in backpack weight, backpack percentage and musculoskeletal discomfort were studied using Mann-Whitney U test; Kruskal-Wallis test was used to study the influence of backpack carrying style on musculoskeletal discomfort; and Spearman rho correlation to determine the relationships between backpack weight, backpack to body weight ratio, age and pain intensity. There were 882 boys and 903 girls recruited into the study. Shoulder pain was the most prevalent discomfort (63.5 %), and pain was significantly higher in girls (p = 0.013). There were weak relationships between pain intensity, body weight and backpack to body weight ratio (r range 0.433-0.442; p < 0.001), and a weak negative relationship between pain intensity and age [r = -0.135; p < 0.001; 95 % confidence interval (CI) -0.168, -0.075]. There was a strong relationship between backpack weight and age (r = 0.892; p < 0.001; 95 % CI -0.129, -0.013); however, there was a weak relationship between backpack weight and body weight (r = 0.136; p < 0.001). Prevalence of shoulder pain was high, particularly among the girls, in this sample. We suggest that factors other than the weight of backpack may predispose to musculoskeletal pain. Parents, teachers and clinicians can influence the mode of carrying backpack by secondary school students.