Background Functional near infrared spectroscopy (fNIRS) provides a direct and quantitative assessment of cortical haemodynamic function during a cognitive task. This functional neuroimaging modality may be used to elucidate the pathophysiology of psychiatric disorders, and identify neurophysiological differences between co-occurring psychiatric disorders. However, fNIRS research on borderline personality disorder (BPD) has been limited. Hence, this study aimed to compare cerebral haemodynamic function in healthy controls (HC), patients with major depressive disorder (MDD) and patients with BPD. Methods fNIRS signals during a verbal fluency task designed for clinical assessment was recorded for all participants. Demographics, clinical history and symptom severity were also noted. Findings Compared to HCs (n = 31), both patient groups (MDD, n = 31; BPD, n = 31) displayed diminished haemodynamic response in the frontal, temporal and parietal cortices. Moreover, haemodynamic response in the right frontal cortex is markedly lower in patients with MDD compared to patients with BPD. Interpretation Normal cortical function in patients with BPD is disrupted, but not as extensively as in patients with MDD. These results provide further neurophysiological evidence for the distinction of patients with MDD from patients with BPD.