Different dysfunctional emotion regulation strategies are observed in patients with borderline personality disorder (BPD) and comorbid eating disorders (EDs) who report non-suicidal self-injury (NSSI). The objective of this study was to investigate the relationship of two well-defined emotion regulation strategies (i.e. expressive suppression and cognitive reappraisal) and dissociation with NSSI. The participants were sixty-eight women diagnosed with BPD and comorbid ED. A cross-sectional research design was used, and clinical interviews and self-report questionnaires were administered to collect data. Multiple regression was conducted to analyze the relationship of two emotion regulation strategies and dissociation with NSSI. According to the results, for low cognitive reappraisal scores, an increase in dissociation leads to an increase in NSSI; however, as cognitive reappraisal increases, higher dissociation is associated with fewer NSSI. When expressive suppression is low, an increase in cognitive reappraisal is associated with a decrease in NSSI; however, as suppression increases, a higher cognitive reappraisal has less effect on decreasing NSSI. These findings indicate that cognitive reappraisal reduces the harmful effects that dissociation has on NSSI, and that expressive suppression interferes with the beneficial effects of cognitive reappraisal on NSSI. Therefore, targeting expressive suppression before cognitive reappraisal is conducted may enhance treatment outcomes for patients with BPD and comorbid ED.