Background: Insomnia is a widespread complaint in the general population. Wendan decoction has been widely applied in the treatment of primary insomnia. However, to our knowledge, there has been no systematic review or meta-analysis of randomized controlled trails regarding the effectiveness of this treatment. Here, we provide a protocol to evaluate the efficacy and safety of Wendan decoction for primary insomnia. Methods and analysis: Relevant randomized controlled trials in 5 English databases [EMBASE, the Cochrane Central Register of Controlled Trials (Cochrane Library), PubMed, the Allied andComplementaryMedicine Databases (AMED), and the Cumulative Index to Nursing and Allied Health Literature (CINAHL)], 4 Chinese databases [Chinese Biomedical Literature Database (CBM), Chinese Medical Current Content (CMCC), China National Knowledge Infrastructure (CNKI), and Wanfang Database] will be comprehensively searched by 2 researchers in October 2017. The therapeutic effects according to the Pittsburgh Sleep Quality Index (PSQI) will be accepted as the primary outcomes. We will use RevMan V. 5.3 software as well to compute the data synthesis carefully when a metaanalysis is allowed. Results: This study will provide a high-quality synthesis of current evidence of Wendan decoction for primary insomnia from several aspects including PSQI, the total scores of the Insomnia Severity Index (ISI), syndrome according to standards for assessing Traditional Chinese medicine and adverse events. Conclusion: The conclusion of our systematic review will provide evidence to judge whether Wendan decoction is an effective intervention for patient with primary insomnia. Ethics and dissemination: The outcomes of this systematic review will offer implications of the use of Wendan decoction treatment for primary insomnia patients. This knowledge informing recommendations will be provided by researchers who are interested in the treatment of primary insomnia. The results of this study will be disseminated through presentation at a conference and publication of the data in a peer-reviewed journal. PROSPERO registration number: PROSPERO CRD 42017065664.