<p>School alienation, understood as a negative attitude toward school-related activities and the school community, increases across schooling and poses challenges for teachers and educational professionals. In this process, students’ perceptions of teacher justice play an important role. Drawing on data from 15 focus groups with <i>N</i> = 134 Swiss students (four schools from two school districts) in the binational project School Alienation in Switzerland and Luxembourg (SASAL), this study investigates how aspects of school alienation are associated with perceived teacher injustice. At two measurement points covering the transition from primary to lower secondary education, students were asked to describe situations of school alienation. Structured content analysis revealed several domains in which experiences central to school alienation co-occurred with perceived injustice, including the student–teacher relationship, handling of peer conflicts, learning processes, assessments, disciplinary measures, allocation, and transition. Distinct patterns emerged between school levels, reflecting performance heterogeneity in primary classes and the subject-teacher system in lower secondary education as relevant to the association between school alienation and teacher injustice. The findings emphasize the value of fostering a just, safe, and supportive school environment and building trusting relationships to positively shape students’ perceptions of school experiences and mitigate school alienation.</p>