["Journal of Child Psychology and Psychiatry, EarlyView. ", "\n\nBackground\nThe transition from primary‐to‐secondary school significantly impacts students' well‐being. However, existing research provides limited insight into the long‐term impact of school transition on well‐being, and no studies have disentangled age‐related changes from transition‐specific effects. This study leverages a natural experiment, where an educational reform resulted in two different age cohorts transitioning simultaneously, to disentangle age effects from transition effects on student well‐being.\n\n\nMethods\nThis study analyzed longitudinal data from the Well‐being and Engagement Collection census (2019–2025) in South Australia. Participants were two cohorts of students who simultaneously started secondary school in 2022: one transitioning at Year 7 and the other at Year 8. Well‐being was measured across eight domains. Linear mixed‐effects regression models examined transition effects and tested interactions with sociodemographic factors.\n\n\nResults\nA total of 20,910 participants (Male: 52.1%, Age in 2019: 9.7 ± 0.6) contributing 104,800 observations (5.0 responses/participant) across the 7 years were included. In the first 2 years post‐transition, well‐being experienced adverse changes across all domains (marginal effects for positively‐worded measures: −0.44 to −0.18; negatively‐worded measures: 0.08 to 0.13). The largest declines were observed in cognitive engagement (−0.44) and perseverance (−0.31). Younger and older cohorts experienced similar adverse changes; however, the younger cohort showed a larger well‐being decline in the second‐year post‐transition. Females experienced more pronounced declines than males. The well‐being decline among students residing in remote and very remote areas persisted until the third year after the transition.\n\n\nConclusions\nSchool transitions negatively affect students' well‐being, with impacts that persist for more than 2 years. This decline was largely attributable to the school transition rather than age‐related progression. Females and students residing in remote areas experienced greater declines in well‐being than their counterparts. These findings highlight the need for transition‐specific support strategies for vulnerable groups that extend beyond the first year of secondary schooling.\n\n"]