School absenteeism, particularly among junior high school students, has increased annually in Japan. This study demonstrates the relationship between subjective adjustment to school life and students’ absenteeism. Data were collected from 17,378 junior high school students in Japan. A longitudinal design was used for the study. Teachers were asked to distribute the Adaptation Scale for School Environments on Six Spheres (ASSESS) questionnaire to junior high school students and ask the students to fill out the questionnaire at the beginning of the 2014 academic year in April 2014, and the relationship between their subjective adjustment and absenteeism as measured by the total number of absent days during the 2014 academic year was evaluated by logistic regression and a survival analysis model. Low life satisfaction was associated with absences. The corresponding odds ratio (OR) was higher for seventh graders (OR 3.29, confidence interval (CI): 2.41–4.48, hazard ratio (HR) 5.57, CI: 3.51–8.84) than for students in other grades. Interpersonal relationships were significantly related to absenteeism for seventh and eighth graders in the group with scores less than 39 points. Lower adjustment to learning seemed to be related to absenteeism for seventh and eighth graders. For effective interventions, a well-designed study that uses detailed information regarding life-related covariates is necessary.