Background: Negative outcomes of peer dislike may be especially severe in early adolescence, when peers play a crucial role in individual adjustment. However, it remains unclear whether peer dislike predicts later emotional and motivational aspects of school adjustment, and if the negative outcomes are more pronounced in certain gender contexts. Objective: Therefore, this study focused on longitudinal effects of peer dislike on academic motivation, school attachment, and feelings of safety at school, and examined the role of gender context of the dislike. Methods: Early adolescents (N = 751; 50.6% female; Time 1 M[subscript age] = 12.9 years, SD = 5 months) filled a set of self-reported and peer nomination procedures at two time points (with a six-month interval). Results: Multilevel modeling showed that while peer dislike was negatively associated with school attachment and feelings of safety at school only concurrently, it had both concurrent and longitudinal negative associations with academic motivation. Importantly, being disliked by peers in the fall negatively predicted academic motivation six months later. The longitudinal effect of peer dislike was consistent across boys and girls, as well as across same- and cross-gender peer dislike. Conclusions: The findings show that targeted interventions are needed for all students who experience peer dislike, regardless of the gender context of the dislike. In addition to fostering respectful and inclusive relations in classrooms, it is important for teachers to offer specific support for academic motivation to students who experience peer dislike in order to keep them academically engaged and successful.