Introduction Functional constipation (FC) is a common digestive system disease, with an uptrend in morbidity and mortality, resulting in huge social and economic losses. Although the guidelines recommend lifestyle intervention as a first-line treatment, lifestyle intervention is not widely used in clinic. Inulin can be used as the basic material of functional food. Clinical studies have shown that inulin supplementation is associated with increased frequency of bowel movements, but has certain side effects. Therefore, the efficacy and safety of inulin in the treatment of FC need to be further evaluated. Methods and analysis We will search Medline, Web of Science, Embase, China National Knowledge Infrastructure Database, Wanfang Database and China Biomedical Literature Database. We will also search the China Clinical Trial Registry, the Cochrane Central Register of Controlled Trials and related conference summaries. This systematic review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. RevMan V.5.3.5 will be used for analysis. Ethics and dissemination This systematic review will evaluate the efficacy and safety of inulin supplementation for the treatment of FC. All included data will be obtained from published articles, there is no need for the ethical approval, and it will be published in a peer-reviewed journal. Due to lack of a new systematic review in this field, this study will combine relevant randomised controlled trials to better explore the evidence of inulin supplementation in the treatment of FC and guide clinical practice and clinical research. PROSPERO registration number CRD42020189234.