Objectives: Key neurobiological factors contribute to vulnerability to nonsuicidal self-injury (NSSI) among adolescents and how they respond to treatment targeted to reduce such behaviors. This study aims to examine differences in intrinsic functional connectivity between adolescents with NSSI and healthy controls (HCs) and to identify baseline connectivity markers that predict improvements in NSSI after psychotherapy. Methods: Adolescents aged 12–17 (n = 24) with repetitive NSSI along with demographically similar HCs (n = 16) underwent resting-state functional MRI scanning after which patients received up to 4 months of psychological treatment. A seed-based approach was used to examine baseline between-group differences in intrinsic functional connectivity of the amygdala and the medial prefrontal cortex (mPFC). Further analyses examined the associations between intrinsic functional connectivity at baseline and improvement in NSSI after psychological treatment. Results: Compared with HCs, adolescents with NSSI showed significantly reduced connectivity between the amygdala and the anterior cingulate cortex, subcallosal cortex, and paracingulate gyrus, as well as between the amygdala and a cluster encompassing the right planum temporale and right insula. Adolescents with NSSI, compared with HCs, also showed reduced connectivity between the mPFC and two clusters: one located in the precentral and postcentral gyri and another in the left insula. After treatment, 50% of patients reported fewer NSSI episodes compared to baseline, which was considered as improvement. Stronger negative amygdala-prefrontal connectivity was associated with greater posttreatment improvement in NSSI. Conclusions: Adolescents with NSSI may have aberrant amygdala and mPFC connectivity compared with HCs. Furthermore, stronger baseline negative amygdala-prefrontal connectivity may predict greater improvement in NSSI after psychological intervention. Given that no prior study has used resting-state functional connectivity to predict response to psychological treatment in adolescents with NSSI, replication of these findings is needed.