Vestibular migraine (VM) has emerged as one of the major vestibular syndromes. Although probiotics have exhibited beneficial effects on migraine headache, its effect on VM is not clear. This trial aimed to investigate the treatment efficacy of the probiotic Lactobacillus casei Shirota (LcS) on symptoms of VM. 247 VM patients were enrolled, of which 204 eligible patients receiving either LcS or placebo on a daily basis completed the 4 month study. They were re-visited at 2 and 4 months after study initiation to assess treatment outcomes. The primary endpoints were vestibular symptoms, evaluated by the number of vertiginous attacks during the past week, the Vertigo Severity Score (VSS), and Dizziness Handicap Inventory (DHI) scores. The secondary endpoints were anxiety and depressive symptoms, evaluated using Beck Anxiety Inventory (BAI) and Beck Depression Inventory (BDI) scores. Efficacy of LcS over placebo was not obvious at 2 month follow-up. At 4 month follow-up, while both LcS and placebo groups of VM patients displayed alleviated symptoms, the extents of the improvements were significantly better in LcS group than those of placebo group, with regard to vestibular symptoms using DHI and VSS, as well as anxiety and depressive symptoms using BAI and BDI. Although placebo effect cannot be ignored in intervention for VM patients, the probiotic LcS still exhibits considerable efficacy against VM symptoms over a 4 month study period, supporting further clinical study of a larger and more diverse cohort.