Physical education (PE) is an essential school subject due to its potential to promote well-being and health in all children. Yet, PE stands out among other subjects in terms of truancy. This study is one of the first to examine if unexcused absence from PE is associated with early adolescents' body image and autonomous motivation towards PE. A total of 526 Swedish 6th graders (Mage = 12.28, SD = 0.31) reported the frequency of unexcused absence from PE and answered questions about aesthetic and functional body image, social physique anxiety, and autonomous motivation. Findings showed that unexcused absence from PE was associated with less autonomous motivation and higher social physique anxiety. Participants who had never been absent reported higher functional body image investment and satisfaction. Analyses showed that whereas the aesthetic aspects of body image were associated with decreased autonomous motivation toward PE, functional aspects predicted higher autonomous motivation. The study sheds novel light on the links between absence from PE, body image, and autonomous motivation. As absence may have real-life practical effects for school achievement, health, and well-being, the findings demonstrate the importance of mitigating social physique anxiety and promoting an inclusive and body positive PE context early on.