Studies of neurobiological mechanisms in borderline personality disorder (BPD) have increased our understanding of the pathophysiology of its development and course. Less is known about how psychotherapy may influence these neurobiological factors, and also whether biomarkers may predict psychotherapy outcomes. We conducted a systematic review using PRISMA guidelines. Fourteen studies providing data from 467 participants diagnosed with BPD met inclusion criteria to: (a) investigate biomarkers predicting response to psychotherapy for BPD; or (b) examine neurobiological factors altered by psychotherapy. Neuroimaging studies (n = 11) used mostly functional magnetic resonance imaging methods to scope brain regions related to emotion regulation and cognitive control. Three studies examined genetic or neuroendocrine markers. The evidence suggests that psychotherapy alters neural activation and connectivity of regions subserving executive control and emotion regulation. Additionally, hypoactivation in prefrontal and cingulate regions predicted treatment response. Further work in this area may inform personalised treatment approaches in clinical practice for BPD through elucidating neural mechanisms of evidence-based psychotherapy.