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School absenteeism (futōkō) has increased substantially in Japan over the past decade, yet empirical research based on students who are actually experiencing prolonged school absence remains limited. This study aimed to (a) classify types of school absenteeism based on students’ self-reported reasons for absence, (b) identify factors associated with students’ willingness to maintain contact with teachers during home visits, and (c) examine the consequences of school absenteeism for parents, with particular attention to gender differences. Questionnaire data were collected from 211 student–parent pairs in a large urban municipality in Japan. Hierarchical cluster analysis identified three subtypes of school absenteeism: the Unclear-Reason Type, the Outside-Interest Type, and the Interpersonal-Conflict Type, with the Unclear-Reason Type constituting the largest proportion across both elementary and junior high school levels. Multiple regression analyses revealed developmental differences in factors associated with students’ willingness to meet teachers during home visits. Among elementary school students, the overall model was significant, but only communication mediated through parents showed a marginal positive association with willingness to meet teachers, whereas no trust-related teacher behaviors demonstrated unique effects when controlling for other variables. In contrast, among junior high school students, advance notification prior to home visits emerged as the strongest predictor of willingness to meet teachers, highlighting the importance of predictability and autonomy-respecting practices during early adolescence. In addition, school absenteeism was associated with substantial changes in parents’ daily lives and social participation, and, for some families, aspects of employment. Mothers reported higher levels of impact than fathers in social and school-related domains, while many parents also reported increased time spent interacting with their child. Together, these findings highlight the heterogeneity of school absenteeism in Japan and underscore the importance of developmentally sensitive school–student contact practices, as well as the need to address school absenteeism as a family-level issue that can intersect with gendered roles.