Background: Functional constipation (FC) is a common functional gastrointestinal disorders (FGIDs) which has a major impact on the quality of life. Acupuncture is widely used as an alternative and complementary medicine (CAM) for FC, but the available evidence of its effectiveness is scarce. Therefore, we will perform a randomized controlled trial to determine whether acupuncture improves symptom and quality of life in FC patients more effectively than sham acupuncture or gastrointestinal prokinetic agent. This article will report the protocol of the trial. Methods: The current trial is a multicenter, randomized, three-arm controlled study undergoing in China. About 243 people who aged from 18 to 65 years with FC will be recruited in this study. These participants will be randomly allocated into three treatment groups, including electro-acupuncture (EA), Mosapride (M) and Mosapride & Sham Electro-acupuncture (MS) groups in a 1: 1: 1 ratio. Both the EA and sham EA receives 16 sessions of needling at Quchi (LI11) and Shangjuxu (ST37) during 4 weeks of treatment, and a follow-up period of 4 weeks. These groups will be compared on the primary outcomes of the number of times of defecation at baseline and 2, 4, 8 weeks after randomization. The secondary outcome measures include: stool consistency, intensity of defecating difficulty, MOS item Short Form health survey (SF-36), Self-Rating Anxiety Scale (SAS), Self-rating Depression Scale (SDS), and the validated Patient Assessment of Constipation Quality of Life (PAC-QOL). These outcomes are measured at baseline and 2, 4 weeks after randomization, but SF-36 is measured at baseline and 4 weeks after randomization. Discussion: This study will supply significant evidence for using acupuncture to treat FC, and will help us to observe whether it is a therapeutic effect rather than a placebo effect.