Introduction: Neural alterations in limbic and prefrontal circuits in association with self-injurious behavior have been studied primarily in adult borderline personality disorder (BPD). In adolescent patients, research is still sparse. Here, we used resting functional near-infrared spectroscopy (NIRS) to examine oxygenation of the pre- frontal cortex (PFC) and its association with symptom severity in adolescents engaging in non-suicidal self-injury (NSSI) and matched healthy controls (HC). Methods: Adolescents (12–17 years) with recurrent episodes of NSSI (n = 170) and healthy controls (n = 43) performed a low-demanding resting-state vanilla baseline task. Mean oxygenation of the PFC and functional connectivity within the PFC, were measured using an 8-channel functional NIRS system (Octamon, Artinis, The Netherlands). Various clinical variables derived from diagnostic interviews and self-reports were included in statistical analyses to explore potential associations with PFC oxygenation and connectivity. Results: Adolescents with NSSI showed significantly decreased PFC oxygenation compared to HC, as indexed by oxygenated hemoglobin. Lower PFC oxygenation was associated with greater adverse childhood experiences and less health-related quality of life (HRQoL). While there was no evidence for alterations in PFC connectivity in adolescents engaging in NSSI compared to HC, increased PFC connectivity in the full sample was associated with greater adverse childhood experience, greater BPD pathology, greater depression severity and psychological burden in general, as well as lower HRQoL. Conclusion: This study is the first to examine PFC oxygenation using NIRS technology in adolescents engaging in NSSI. Overall, results indicate small effects not specific to NSSI. Clinical implications of these findings and recommendations for further research are discussed.