Background: Recently the gut microbiota has attracted significant interest in psychiatric research due to the observed bidirectional gut–brain communication. A growing body of evidence from preclinical work has suggested that probiotics may be effective in reducing stress and anxiety and alleviating low mood. It is unclear to what extent these effects are seen in clinical populations. We aimed to identify all published evidence on the efficacy of probiotics as treatment for depression in clinically depressed populations. Methods: Randomized controlled trials of patients with depression where probiotics were used as supplementary or standalone treatment were considered eligible. A literature search with the terms ( probiotic* OR bacteria OR Lactobacillus OR Bifidobacterium) AND depress* was performed in PubMed and Web of Science. Data on study population characteristics, treatment effectiveness, tolerability and risk of bias were extracted from eligible studies. A random effects model was used for meta-analyses. Results: Only three studies met inclusion criteria (229 individuals randomized), two of which administered probiotics as a supplementary treatment to antidepressants and one as a standalone treatment. Upon removal of the latter study from the meta-analysis due to clinical heterogeneity, there was an overall positive effect of probiotics on depressive symptoms (standardized mean difference = 1.371, 95% confidence interval 0.130–2.613). Conclusions: There is limited evidence for the efficacy of probiotics in depression at present, although there may be a beneficial effect of probiotics on depressive symptoms when administered in addition to antidepressants. Further studies are required to investigate this and explore potential mechanisms.