BACKGROUND: Functional constipation (FC) is a common functional gastrointestinal disorder, which brings many negative impacts to the children's daily life. Pediatric Tuina has been proved to be a potential therapy for FC. However, the evidence for its effectiveness and safety is insufficient due to the lack of high-quality study. This study aims to evaluate the efficacy and safety of pediatric Tuina for children with FC. METHODS/DESIGN: This study is a randomized, controlled, multicentre, clinical trial. We will include 176 children with FC from five hospitals. The participants will be randomly allocated into two groups: the pediatric Tuina group and the Medilac-Vita group. This study will include a 1-week actual treatment period and a 2-week follow-up period. Primary outcomes are weekly spontaneous bowel movements and weekly complete spontaneous bowel movements. The secondary outcomes are effective rate, stool form, distress sensation, and glycerine enema rate. The assessment will be performed each week. Adverse event will be monitored in the treatment period and follow-up period. DISCUSSION: This study is designed to evaluate the efficacy and safety of pediatric Tuina for children with FC, and we hypothesize that pediatric Tuina is more effective than probiotics. It will provide reliable evidence and support for the treatment of FC by pediatric Tuina. TRIAL REGISTRATION: This protocol was registered in the Chinese Clinical Trial Registry (ChiCTR2100046485). .