Purpose: Guided by the conception that amotivation is a multidimensional construct, the present study aimed to evaluate gender as a moderator of relationships between different dimensions of perceived teachers’ controlling behavior and amotivation in high school physical education. Method: A total of 419 students (246 girls and 173 boys) completed questionnaires assessing their relevant psychological constructs. To detect gender differences, a multi-group structural equation modelling was employed with restrictions placed on the structural paths across genders. Results: The results revealed that girls showed overall higher amotivation and more strength than boys in associations of perceived negative conditional regard and intimidating behavior from teachers with amotivation, whereas boys demonstrated more strength than girls in the association of perceived teachers’ controlling use of praise with amotivation. Discussion/Conclusion: These gender differences should be acknowledged and instructionally addressed during teaching and learning to diminish students’ lack of motivation in physical education.