The Psychological Sense of School Membership (PSSM) scale is widely used to measure school belongingness among adolescents. However, previous studies identify inconsistencies in factor structures across different populations. The factor structure of the PSSM has yet to be examined with American Indian/Alaska Native (AI/AN) youth, a population of keen interest given reports of their educational and health disparities, and the potential of belongingness as a protective factor against risk behaviors. Thus, this study examined the factor structure of the PSSM in two samples of AI adolescents (N = 349). The two main aims of this study were to 1) determine if a comparable factor structure exists between the two AI groups and 2) examine the factor structure of the PSSM for use in AI/AN populations. Randomization analysis was used to test research aim one, and exploratory factor analysis was used to test research aim two. Analyses revealed that comparable factor structures existed based on responses from the two AI groups. Analyses also identified two factors: school identification/peer support and connection with teachers. Moreover, negatively worded statements were found to be unreliable and were removed from the final scale, reducing the PSSM to 13 items. Findings from this study will assist researchers and clinicians with assessing sense of school belongingness in AI/AN adolescents and with appropriately interpreting aspects of belongingness for this population.