Purpose: The purpose of this study was two-fold: to examine the motivational profiles of secondary school students in physical education classes, and to examine the associations between the students' motivational profile characteristics and positive and negative affective experiences. Methods: A total of 1,570 students from Hong Kong were invited to complete four questionnaires: the Perceived Locus of Causality Scale, the Psychological Needs Satisfaction Scale in Physical Education, The Psychological Needs Thwarting Scale in Physical Education, and the International Positive and Negative Affect Schedule Short Form. A two-step cluster analysis was performed to explore the motivational profiles while MANOVAs were conducted to examine the criterion validity of the cluster analysis and differences on affective outcomes between motivational profiles. Results: Four motivational profiles were identified: non-self-determined, moderate controlled and low autonomous (Mod C-Low AU), high controlled and moderate autonomous (High C-Mod AU), and self-determined. The results revealed that students in different profiles reported different affective experiences. Conclusion: Motivational profiles based on self-determination theory may be better explained from a psychological needs perspective, and students in different profiles may undergo different affective experiences.