Oral intake of probiotics has been shown to positively impact depression, anxiety, stress and cognition. Recently, an effort was made to more objectively assess their impact on brain structure and function. However, there has been no exhaustive systematic assessment of outcomes of these studies, nor the techniques utilised. Therefore, we performed a systematic review on randomised, placebo-controlled trials assessing the effects of oral probiotic interventions on brain health by imaging or electrophysiology techniques in human adults. Of 2307 articles screened, 26 articles comprising 19 studies, totalling 762 healthy subjects or patients with various diseases, were ultimately included. The quality of most studies was high. Overall, probiotic intake appears to modify resting state connectivity and activity, decrease involvement of several brain regions during negative emotional stimulation, and improve sleep quality. Several studies found correlations between brain outcomes and clinical symptom ratings, supporting the relevance of brain imaging and electrophysiology techniques in this field.