Objective: The aims of this study were: (i) to investigate the effect of functional magnetic stimulation on total colonic transit time in patients with Parkinson's disease; (ii) to compare the changes in dynamic recto-anal behaviour during filling and defaecation in response to this regimen; and (iii) to study the carry-over effects with a 3-month follow-up. Design: A longitudinal, prospective before-after trial. Subjects: Sixteen patients with Parkinson's disease enrolled in this study. No subject withdrew from the study as a result of serious adverse events. Methods: A 3-week magnetic conditioning protocol, consisting of a 20-min stimulation session twice daily. Colonic transit time, Knowles-Eccersley-Scott Symptom Questionnaire and the dynamics of defecography were carried out before the intervention and on the final day of the protocol. Results and conclusion: There was a statistically significant reduction in colonic transit time and in the questionnaire score following the intervention. The difference in the anorectal angles between resting and evacuating process and the changes in pelvic floor descent all reached significance after the intervention. The therapeutic effects that achieved significance remained constant in the 3-month follow-up result. Functional magnetic stimulation may facilitate colonic motility in Parkinson's disease and straighten the anorectal angle, allowing smooth access of rectal contents to the anal canal.