Most prior studies on academic motivation of intellectually gifted children focused only on intrinsic motivation. To gain insight into the full scope of intellectually gifted students' motivation, differences between clinically diagnosed gifted students and their classmates in multiple motivational dimensions (intrinsic, identified, introjected, and external regulation, and amotivation) were examined across two school years. Using both variable-centered and person-centered techniques, we examined differences in separate motivational dimensions as well as differences in configurations of motivational dimensions (‘profiles’). A sample of 1438 primary school students in Grade 3–5 (5.5% clinically diagnosed as gifted with an IQ > 120) participated. They filled out motivation questionnaires pertaining to their regular class during two waves across two school years. Gifted students reported more favourable motivation at Wave 1 but lost this advantage over time. Specifically, they demonstrated more intrinsic motivation at Wave 1, but a decrease in identified regulation, and a stronger increase in external regulation and amotivation from Wave 1 to Wave 2. Similarly, gifted students were more likely to transition from theoretically more favourable to less favourable profiles. These findings suggest that children who are clinically diagnosed as gifted are at risk for developing unfavourable motivational patterns toward the end of primary school. Educational relevance statementMotivation for school plays a pivotal role in students' school engagement and achievement. This is also the case for intellectually gifted children. Just like other children, motivation enables them to translate their abilities into achievement. Intellectually gifted students in primary school may particularly be at risk of unfavourable motivational developments because it can be difficult for regular schools to provide an optimally challenging learning environment for them. This study aimed to get a full understanding of the motivational dynamics of intellectually gifted children in regular classes. This would be a step toward developing more targeted interventions that can address motivational problems encountered by gifted students in regular classes.The findings of this study indicated that, clinically diagnosed gifted children initially reported more favourable motivation, but lost this advantage over time. Toward the end of primary education, they were more likely than other children to show a decrease in external motivation and amotivation.These findings are of great practical importance. If teachers can identify students who start to become less motivated for school, it may be easier to intervene and prevent motivational problems and subsequent underachievement later on. To identify students who are at risk of developing an unfavourable motivational pattern, teachers or other educational professionals could regularly assess their students' motivation or engage in talks with their students about their motivation. Additionally, prior research suggests teaching practices and interventions which support students' need for autonomy, structure, and relatedness are likely to foster students' motivation for school, for gifted students as well as other students.