Introduction Bacterial vaginosis (BV) is a highly prevalent vaginal polymicrobial disorder commonly encountered in women of childbearing age. Therapy with only recommended antibiotics results in low cure rates and unacceptably high recurrence rates. The use of probiotics as a complementary approach for use with antibiotics for the treatment of BV remains unclear. This review aims to assess the efficacy of lactobacilli administered intravaginally in conjunction with antibiotics for the treatment of BV. Methods and analysis The Cochrane Central Register of Controlled Trials in The Cochrane Library, Cochrane Library of Systematic Reviews, Medline/PubMed and Embase will be used to search for articles from database inception to November 2016. Randomised controlled clinical trials using lactobacilli administered intravaginally in conjunction with antibiotics to treat BV will be included. Primary outcome will be the BV cure rate. The recurrence rate will be examined as secondary outcome. Two reviewers will independently select trials and extract data from the original publications. The risk of bias will be assessed according to the Cochrane Risk of Bias tool. We will perform data synthesis using the Review Manager (RevMan) software V.5.2.3. To assess heterogeneity, we will compute the I-2 statistic. Ethics and dissemination This study will be a review of published data and it is not necessary to obtain ethical approval. Findings of this systematic review will be published in a peer-reviewed journal.