This longitudinal study tracked the trajectories of school well-being of gifted and non-identified early adolescents before and through the COVID-19 pandemic (2019-2022). We used a prospective cohort panel design that followed students (N =1,033) from grade 3 until the end of grade 6. Three aspects of school well-being were examined through both hedonic and eudaimonic views of well-being: school liking, peer connectedness, and academic motivation. Longitudinal multilevel modeling showed that the pandemic was associated with negative shifts in students' academic motivation, but not with school liking or peer connectedness. When considering students’ gifted status, students gifted in cognitive superior abilities, reading, or math showed similar trajectories of school liking but greater declines in peer connectedness than their non-identified peers, especially during the pandemic years. The gifted students also showed a slower rate of growth in math expectancy than non-identified students over time, regardless of the state of the pandemic. Students gifted in math experienced a shift from high and stable academic motivation in the pre-pandemic years to a decline during the pandemic, while other students experienced a shift from growth in academic motivation before the pandemic to maintaining the same or lower levels during the pandemic. Our findings shed light on gifted early adolescents’ resilience and vulnerability during transitions and upheavals like the pandemic, illuminating future research directions on how schools can differentiate their adaptation and support for gifted students at a uniquely important time in their development.