The purpose of the study was to examine whether higher levels of adolescents’ perceptions of intimidating behavior and negative conditional regard by the PE teacher, thwarting of the psychological needs for autonomy, competence, and relatedness, fear of failure, contingent self-worth, and challenge avoidance are linked to the presence of developmental coordination disorder (DCD) in physical education. Motor proficiency was evaluated using the Movement Assessment Battery for Children (2nd ed.) in a sample of 336 adolescents. Students’ perceptions on motivational constructs were measured via self-report questionnaires and compared between adolescents with DCD and typically developing peers. Independent of gender, presence of DCD was linked to significantly higher levels of the above negative motivational constructs. Independent of DCD, boys reported significantly higher levels on all negative motivational constructs than girls except contingent self-worth. Among adolescents with DCD, boys reported greater autonomy and competence thwarting compared to girls. Within boys, those with DCD reported greater levels of intimidation, autonomy thwarting, competence thwarting, and fear of failure compared to typical boys. No differences emerged between girls with and without DCD. Adolescents with DCD seem to report higher levels of negative motivational experiences in school physical education compared to their typically developing peers. The present study extends the evidence base of psychosocial variables of a motivational nature in physical activity linked to the presence of DCD.