Background/Aims Psychobiotics are probiotics or prebiotics that, upon ingestion in adequate amounts, yield positive influence on mental health via microbiota-gut-brain axis regulation to modulate the circulating cytokines, chemokines, neurotransmitters, or neurotrophins levels. We have recently shown that a psychobiotic combination (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175; CEREBIOME) significantly improved depression symptoms in patients with depression. Recent animal data suggest the influence of the gut microbiota on brain-derived neurotrophic factor (BDNF), which was shown to correlate with antidepressant response in depressive patients. Therefore, we conducted this exploratory post hoc analysis of BDNF levels to clarify the mechanism of action of this psychobiotic in our cohort. Methods Our study was a double-blind, randomized controlled trial of patients with low-to-moderate depression receiving either a probiotic combination, prebiotic or placebo. From the 110 patients randomized in the trial, 78 were included in this post hoc analysis (probiotic, n = 28; prebiotic and placebo, n = 25). We compared serum BDNF levels from participants at baseline and endpoint, and assessed the Pearson correlation between depression severity and BDNF levels for each intervention. Results We found that post-intervention BDNF levels were significantly different between groups (P < 0.001). Furthermore, BDNF levels increased significantly in the probiotic group compared to both the prebiotic (P < 0.001) and placebo groups (P = 0.021), which inversely correlated with depression severity compared to placebo (ANOVA/ANCOVA, P = 0.012; Pearson, r =-0.79, P < 0.001). In the prebiotic group, BDNF levels reduced but not significantly compared with placebo group (P > 0.05). Conclusion Eight-week supplementation with B. longum and L. helveticus in depressive patients improved depression symptoms, possibly by increasing BDNF levels.