Friendships with classmates play a significant role in student’s development. However, only some friendships are maintained for longer than a school year and their formation depend on many factors. One important factor is gender because gender homophily is consistently found in friendship networks. In addition, there is evidence that same-gender friendships are more stable. In the context of inclusive education, friendship can be considered as one of four key dimensions of social inclusion. While three of these dimensions are assessed from others’ perspective, self-perception of social inclusion focuses solely on the individual students’ view. However, hardly any studies investigated how students’ self-perception of social inclusion is related to friendships, and more specifically, whether and how self-perceived social inclusion is related to changes in friendship networks in the classroom. To contribute to this research gap, friendship networks of 280 students aged 9–11 years (49% girls) in 15 classes of Grade 4 were examined at the beginning and at the end of one school year. Network changes were analyzed with longitudinal social network analyses. Students’ gender and self-perception of inclusion were added as predictors of changes in the friendship networks. The results confirmed gender homophily for formation and stability. The analyses also showed that students who perceived themselves as socially included nominated more best friends at the end of the school year but were not necessarily perceived as best friends by their peers. This highlights the importance of considering different perspectives to better understand social inclusion in classrooms.