In Japan, the increase in school nonattendance during compulsory education has become a significant social issue. Adaptation assistance classes play an important role as public institutions supporting students with school nonattendance, aiming to facilitate re-attendance and promote social independence. Despite the lack of thorough evaluation of their effectiveness, the establishment of these classes has expanded. This study aimed to compare the effectiveness of adaptation assistance classes and the comprehensive support approach in terms of re-attendance, continued attendance, and post-graduation outcomes. Data were collected from databases on students participating in adaptation assistance classes in Tokyo and on students who received comprehensive support through university clinical psychology centers in several prefectures. A total of 452 students with school nonattendance were identified (n = 410 for adaptation assistance classes, n = 42 for comprehensive support) from 1989 to 2020. Propensity score matching was used to compare re-attendance rates, duration of continuous attendance, and post-graduation outcomes. The results indicated that the adaptation assistance class group showed lower favorable scores across all outcomes compared to the comprehensive support group. Based on these findings, the study discussed the necessity of implementing assessment-based support approaches and assigning specialized staff in adaptation assistance classes.