Background:

Continuous schooling and healthy learning during childhood is essential. Therefore, we investigated the risk factors for absenteeism to support at-risk students. This study examined the longitudinal relationship between absenteeism and frequency of school health room usage, academic performance, body mass index, physical fitness, and lifestyle in the first grade of elementary school using accumulated data from elementary and junior high school students. Methods We analyzed 453 students enrolled in the target elementary and junior high schools in January 2022. The analysis used data obtained from the students’ schoolwork. We performed a Cox regression analysis to assess the characteristics associated with absenteeism for 10 days or more, excluding absences due to relatives’ funerals and suspension of attendance. The independent variables were the frequency of use of the health room, grade points of subjects, grade point average of all subjects, body mass index, physical fitness, frequency of physical activity, and days of good sleep. Results A total of 50 students (27 girls, 11.7%; 23 boys, 10.4%) had 10 days or more of absenteeism. The median (1st–3rd quartile) follow-up period for girls and boys was three (2–5) years. After adjusting for potential confounders, the grade point average and frequency of use of school health rooms due to illness were common in both girls (hazard ratio [HR] = 1.252) and boys (HR = 1.261) in the adjusted model. Additionally, three or more days of physical activity per week (HR = 0.047) and six or more days of good sleep were additional predictors for girls. Conclusions Our results suggest that careful monitoring of children with frequent school health room usage, low grade point average, minimal physical activity, and poor sleep quality in the first grade of elementary school and providing them support in dealing with school difficulties may reduce absenteeism.