Several experimental studies suggest a role of the gut microbiota in the pathophysiology of Parkinson’s disease (PD) via the gut-brain axis. In addition, the gut microbiota can influence the metabolism of levodopa, which is the mainstay of treatment of PD. Therefore, modifying the gut microbiota by fecal microbiota transplantation (FMT) could be a supportive treatment strategy. We developed a study protocol for a single center, prospective, self-controlled, interventional, safety and feasibility donor-FMT pilot study with randomization and double blinded allocation of donor feces. The primary objectives are to assess feasibility and safety of FMT in PD patients. Secondary objectives are to explore whether FMT leads to alterations of motor complications and PD symptoms in the short term, determine alterations in gut microbiota composition and donor-recipient microbiota similarities and their association with PD symptoms and motor complications, assess the ease of the study protocol and examine FMT-related adverse events in PD patients. The study population will consist of 16 idiopathic PD patients that use levodopa and experience motor complications. They will receive FMT with feces from one of two selected healthy human donors. Patients will be pretreated with vancomycin and bowel lavage to increase donor feces engraftment, and domperidone to prevent nausea and regurgitation. The FMT will be performed via direct injection of the fecal suspension into the duodenum via a gastroscope. There will be six follow-up moments during three months. Blood will be drawn on three occasions. Physical examination, filling in of questionnaires and a diary, and collection of stool samples are performed at baseline and each in-person follow-up visit (except for the FMT visit). This study was approved by the Medical Ethical Committee Leiden Den Haag Delft (ref. P20.087) and is registered in the Netherlands Trial Register (NL9438). Study results will be disseminated through publication in peer-reviewed journals and international conferences.