There have been a few studies regarding detail of back pain in adolescents with idiopathic scoliosis (IS) as prevalence, location, and severity. The condition of back pain in adolescents with IS was clarified based on a cross-sectional study using a questionnaire survey, targeting a total of 43,630 pupils, including all elementary school pupils from the fourth to sixth grade (21,893 pupils) and all junior high pupils from the first to third year (21,737 pupils) in Niigata City (population of 785,067), Japan. 32,134 pupils were determined to have valid responses (valid response rate: 73.7%). In Niigata City, pupils from the fourth grade of elementary school to the third year of junior high school are screened for scoliosis every year. This screening system involves a three-step survey, and the third step of the survey is an imaging and medical examination at the Niigata University Hospital. In this study, the pupils who answered in the questionnaire that they had been advised to visit Niigata University Hospital after the school screening were defined as Scoliosis group (51 pupils; 0.159%) and the others were defined as No scoliosis group (32,083 pupils). The point and lifetime prevalence of back pain, the duration, the recurrence, the severity and the location of back pain were compared between these groups. The severity of back pain was divided into three levels (level 1 no limitation in any activity; level 2 necessary to refrain from participating in sports and physical activities, and level 3 necessary to be absent from school). The point prevalence was 11.4% in No scoliosis group, and 27.5% in Scoliosis group. The lifetime prevalence was 32.9% in No scoliosis group, and 58.8% in Scoliosis group. According to the gender- and school-grade-adjusted odds ratios (OR), Scoliosis group showed a more than twofold elevated odds of back pain compared to No scoliosis group irrespective of the point or lifetime prevalence of back pain (OR, 2.29; P = 0.009 and OR, 2.10; P = 0.012, respectively). Scoliosis group experienced significantly more severe pain, and of a significantly longer duration with more frequent recurrences in comparison to No scoliosis group. Scoliosis group showed significantly more back pain in the upper and middle right back in comparison to No scoliosis group. These findings suggest that there is a relationship between pain around the right scapula in Scoliosis group and the right rib hump that is common in IS.