Difficulties that junior adolescents (aged 11–13 years old) experience in terms of academic adaptation, which are indicated through school anxiety and academic wellbeing characteristics, often lead to a dramatic decrease in academic performance, behavioral problems, and deterioration of their health. The purpose of this investigation is to determine the structure of characteristics of school wellbeing/ill-being of junior adolescents and their role in variations of school anxiety, which largely define academic adaptation. In this study, based on positive psychology and a systematic approach, the level of distinctiveness of characteristics of school wellbeing is carried out with the help of comparative analysis; the factor structure of these characteristics is identified; the characteristics of wellbeing and their coordinated combinations (factors) are determined as predictors of school anxiety. The sample consisted of 120 students of the 5th–7th grades, aged M = 11.5; SD = 1.04 (49.2% girls, 50.8% boys) who attended Saratov secondary schools. To study the level of school anxiety, we used the Philips’ School Anxiety Scale (SAS), and indicators of school wellbeing were measured with the original scales developed by the authors of the study. Statistical processing of the results was carried out with regression analysis and factor analysis. The results showed that the school wellbeing of junior adolescents forms a complex structure that includes cognitive, personal, emotional, social, and psychophysiological characteristics of school life. It was found that from 16% up to 53% of the deviation of variables characterizing school anxiety is conditioned by the assessment of variables characterizing emotional states, the ability of self-regulation, cognitive capabilities, and interest in learning. The study determined a high level of tension in adolescents in the field of emotions’ self-regulation, unpleasant physical sensations at school, before and after attending school, in the course of planning their school day and reflecting on educational activities. The most powerful factors of school anxiety in junior adolescents are physical distress, low ability to self-regulate and social adaptation, lack of independence in a learning activity, and personal immaturity.