Objectives School-based mindfulness interventions have recently shown promise for treating and preventing mental health issues in young people. However, the literature lacks a high-level perspective of the impact of mindfulness on young people's mental health according to their own first-hand accounts. Therefore, the objective of this study was to conduct the first systematic review and thematic synthesis to rigorously evaluate the qualitative evidence pertaining to students' experiences of school-based MBIs. Methods The following electronic databases were searched for qualitative school-based mindfulness intervention papers published up until the end of March 2019: PubMed, Web of Science, Scopus, ProQuest, and Google Scholar. An assessment of study quality was undertaken using the Critical Appraisal Skills Programme qualitative checklist. Results The initial literature search returned 4102 papers and seven studies met all of the inclusion criteria. The thematic synthesis identified four major themes of (i) using attentional processes to regulate emotions and cognitions, (ii) stress reduction, (iii) improved coping and social skills, and (iv) calming and/or relaxation. Conclusions Findings show that school-based MBIs are experienced by students as having a range of benefits to mental health, including in both preventative and treatment contexts. However, efforts should be made to improve methodological quality, including taking steps to minimise recall bias and provide a greater degree of transparency regarding how students are selected to attend qualitative interviews or focus groups.