Adolescents with low motor competence have diminished perceptions of their physical self and tend to avoid physical activities. This study examined the outcomes of an exercise intervention that focused on improving aerobic fitness, strength, and self-perceptions in the physical domain in adolescents with poor motor coordination. The sample included 35 adolescents with low motor competence, comprising boys (n = 25) and girls (n = 10) ranging in age from 13 to 17 years, who attended two sessions per week in the 13 week exercise intervention study (AMP it up). Physical self-perceptions were measured before and after the intervention using the Physical Self Perception Profile and Perceived Importance Profile. Significant improvements in perceived Physical Condition, Attractive Body and Physical Strength sub domain scores were identified between pre and post-test. Adjusting for age, gender, BMI and attendance, regression analyses revealed that Attractive Body was the strongest predictor of Physical Self Worth at pre-test, joined by Physical Condition at post-test. This exercise intervention had a positive impact on adolescent physical self-perceptions, in particular males, with improvements in those sub domains specifically related to the exercise program. Changes in specific aspects of Physical Self Worth can be facilitated by exercise interventions, after a relatively short period of time, in adolescents with poor motor coordination