Background Fermented foods are a promising yet underexplored intervention for influencing brain function and mental health through the gut–brain axis. Objective The objective of this study was to evaluate the impact of a dairy product fermented with probiotic bacteria on aspects of brain structure and function. Design In a triple-blind, randomised, placebo-controlled trial, 40 healthy women aged 18–55 years were randomised to consume either 130 g per day of a fermented probiotic yoghurt or a placebo for 8 weeks. The primary outcome was the between-group differential change from baseline to week 8 in left hippocampal metabolites, measured using magnetic resonance spectroscopy. Secondary outcomes included changes in brain structure and function, faecal microbiome composition and functional potential, mental health, gastrointestinal symptoms, memory and blood markers of oxidative stress and inflammation. Results There was a between-group difference in the change in average left hippocampal glutathione concentration (mean difference in change: −0.49; 95% CI −0.95 to −0.04), as well as brain volume in the hippocampus and nucleus accumbens, although these results did not withstand correction for multiple comparisons. There were between-group differences in the change in average functional connectivity between the left hippocampus and left frontal pole. There was also a significant between-group change in gut microbiome beta diversity. There were no differences in other secondary measures. Conclusion This study provides preliminary evidence that a probiotic fermented dairy product can modulate hippocampal-related outcomes. Trial registration number ACTRN12622000622707.