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Introduction Chronic endometritis (CE) is regarded as a potential factor contributing to infertility and embryo implantation failure. The cause of CE remains unclear at present, but it might be associated with intrauterine microbial infections. Empirical antibiotic treatment typically consists of a 2-week course of oral levofloxacin combined with oral metronidazole. Currently, there is no research comparing the efficacy of oral levofloxacin versus vaginal metronidazole suppositories in improving pregnancy outcomes for these patients. This study aims to evaluate the effectiveness of combining oral levofloxacin with metronidazole suppositories in the treatment of CE. The goal is to enhance clinical pregnancy rates and live birth rates among patients undergoing in vitro fertilisation (IVF), while concurrently mitigating the incidence of miscarriages.Methods and analysis The trial concerning the combination of levofloxacin and metronidazole suppositories for the treatment of CE is a single-centre, randomised controlled clinical trial. We plan to recruit female patients with CE who are planning to undergo IVF. Following informed consent, eligible participants will be randomly assigned in a 1:1 ratio to receive either daily oral levofloxacin combined with oral metronidazole or oral levofloxacin combined with a metronidazole suppository for 2 weeks until the human chorionic gonadotropin trigger day. All IVF procedures will be carried out routinely at this centre. The primary outcome is the live birth rate after embryo transfer, while the secondary pregnancy outcomes include clinical pregnancy rates and miscarriage rates.Ethics and dissemination This study has been approved by the Ethics Committee of Peking University Third Hospital on 28 June 2024 (Reference No. IRB00006761-M2023857). Written informed consent will be acquired from all participants prior to randomisation. The study findings will be submitted to scientific conferences and peer-reviewed journals.Trial registration number NCT06650540.