Background: Although non-suicidal self-injury (NSSI) has been much less studied than suicidal behavior, NSSI is now recognized as an even stronger predictor of future suicidal behavior than is a past history of this behavior. Understanding risk factors for NSSI is therefore important not only for preventing its occurrence but also for suicide prevention efforts. Relatively little is known about trajectories of NSSI. Furthermore, although emotion dysregulation and other emotional processes have received theoretical and empirical support in the etiology of NSSI, whether they differentiate between heterogeneous trajectories in this outcome remains unclear. We aimed to identify NSSI trajectories in adolescent psychiatric inpatients and emotional processes that differentiate between trajectories. Methods: Participants were 180 adolescents (71.7% female; mean age = 14.89 years, SD = 1.35) from a pediatric psychiatric inpatient facility. Past-30-day NSSI frequency was assessed at patient’s index hospitalization, as well as six, and 12 months after discharge. At baseline, emotion recognition was assessed using a performance-based task, whereas emotion reactivity and emotion dysregulation were assessed using self-report questionnaires. Latent class mixture modeling was used to identify different NSSI trajectories and ANOVAs were used to evaluate emotion processes variables as prospective predictors of NSSI trajectories. Results: Analyses yielded three NSSI trajectories. These included a stable low-frequency group, a moderate-frequency group, and a group characterized by high frequency of NSSI at baseline but resolution of NSSI by 6-month follow-up. After adjusting for multiple comparisons, only emotion regulation at baseline differentiated between the trajectories, with greater overall emotion dysregulation in the initially high-frequency group relative to the stable moderate-frequency group (p < .05), and greater emotional non-acceptance (a facet of emotion dysregulation) characterizing the initially high-frequency group and the moderate-frequency group more than the stable low-frequency group (ps < .05). Conclusions: The current findings suggest that interventions involving emotion regulation with adolescents who engage in NSSI would particularly benefit from a focus on increasing acceptance of emotional experiences.