Objectives: Empirical research investigating self-compassion is a rapidly developing field, and it is potentially crucial in early adolescence. The primary aim of the present study was to psychometrically evaluate the Persian translation of the Self-Compassion Scale Youth version (SCS-Y) and evaluate its factor structure among young adolescents. The second aim was to explore the buffering effect of self-compassion against the negative effect of difficulties in emotion regulation on COVID-19-related anxiety. Methods: A sample of young students (n = 532; mean age 13.57 years) completed an online survey, which included the SCS-Y, Patient Health Questionnaire, Difficulties In Emotion Regulation Scale, Coronavirus Anxiety Scale, Youth Life Orientation Test, Brief Resilience Scale, and Brief 10-Item Big Five Inventory. First-order (six-factor) confirmatory factor analysis (CFA) and bi-factor exploratory structural equation modeling (ESEM) analysis were used to evaluate the factor structure of the SCS-Y. Results: Results showed that the SCS-Y had very good internal consistency (Cronbach’s alpha coefficient: 0.88; McDonald’s omega coefficient: 0.90), composite reliability (0.87), and adequate test–retest reliability after 4 weeks (0.60). The first-order (six-factor) CFA and bi-factor ESEM analysis demonstrated the SCS-Y had excellent dimensionality. Further analysis found negative associations between self-compassion with both depression and neuroticism, and positive associations between self-compassion with both resilience and optimism. Moreover, self-compassion moderated the association between emotion dysregulation and anxiety generated by the COVID-19. Overall, the findings indicated that the SCS-Y had acceptable criterion-related validity, convergent validity, and discriminant validity. Conclusions: The findings provide evidence that the SCS-Y is a reliable and valid instrument for assessing the six factors of self-compassion among younger adolescents. Based on the study’s findings, self-compassion appears to be a protective factor against mental health problems during the COVID-19 pandemic for younger adolescents.