The suicide mortality rate per 100 000 population (SMRP) consistently decreased before the COVID-19 pandemic outbreak in Japan and then unexpectedly increased during the pandemic. However, the underlying mechanisms remain poorly understood. To identify trends in and factors associated with suicidal mortality and motives among students in Japan from 2007 to 2022. In this cross-sectional study, data on SMRPs among Japanese middle-school, high-school, and university students were obtained from the government suicide database Suicide Statistics of the National Police Agency. Age-dependent and temporal fluctuations in annual SMRPs, disaggregated by suicidal motive (7 categories and 52 subcategories), sex, and school, were analyzed using linear mixed-effect and joinpoint regression models, respectively. Total suicide numbers from 2007 to 2022 were as follows: 760 male middle-school students, 635 female middle-school students, 2376 male high-school students, 1566 female high-school students, 5179 male university students, and 1880 female university students. The mean (SD) student populations from 2007 to 2022 were as follows: 1 752 737 (81 334) male middle-school students, 1 675 572 (78 824) female middle-school students, 1 648 274 (67 520) male high-school students, 1 614 828 (60 032) female high-school students, 1 652 689 (32 724) male university students, and 1 229 142 (57 484) female university students. Among male students, the leading motives were school-related factors (underachievement and worrying about the future), followed by family-related and health-related motives. Among female students, school-related and family-related motives decreased, but health-related motives showed an age-dependent increase. The SMRPs of middle-school male students and female students were almost equal (mean [SD], 2.7 [1.0] vs 2.4 [1.4]), but the age-dependent increase in SMRPs among male students was pronounced (mean [SD], high-school vs university male students, 9.1 [2.4] vs 19.6 [3.0]; high-school vs university female students, 6.1 [2.4] vs 9.6 [1.8]). However, the incidence of suicide among high-school students associated with health-related motives was greater in female students. The majority of suicides associated with major impactable suicidal motives (school-related, health-related, and family-related motives) began increasing before the pandemic. Changes in SMRP associated with interpersonal relationships, such as conflict with classmates or parents, were not significant, but the rates increased greatly during the pandemic. School-related, health-related, and family-related problems were major motives, whereas the impacts of health-related and family-related motives increased and decreased with age, respectively. Notably, most SMRPs associated with major impactable motives (underachievement, conflict with a parent or classmate, and mental illnesses) had already begun increasing in the late 2010s, indicating that recent increasing SMRPs among school-aged individuals were associated with pandemic-related factors and other factors affecting this generation before the pandemic. It may be inappropriate to uniformly apply research findings based on school-aged individuals to school-based suicide prevention programs for students in middle school, high school, and university.