Background The aim of this study was to characterize patients who ingested multiple rare-earth magnets, reveal the harm of rare-earth magnet foreign bodies in the digestive tract, and develop a clinical management algorithm. Methods This was a retrospective review of patients with rare-earth magnet foreign bodies in the digestive tract admitted to a university-affiliated pediatric medical center in China, between January 2016 and December 2019; the subset of medical data evaluated included clinical symptoms, signs, treatments and outcomes. Results A total of 51 cases were included in this study, including 36(70.6%) males and 15(29.4%) females. The magnets were passed naturally in 24(47.1%) patients and removed by intervention in 27(52.9%) patients, including five (9.8%) cases by endoscopy and 22(43.1%) cases by surgery. Twenty-two (43.1%) patients cases had gastrointestinal obstruction, perforation, and fistula. Compared with the non-surgical group, the proportion of males in the surgical group was higher (21/23 vs 15/28, p=0.004), and the time from ingestion to arriving at the hospital was longer (80(72) vs 26(5), hours, p=0.008). Conclusions Magnets are attractive to children, but lead to catastrophic consequences including gastrointestinal obstruction, perforation, and surgical interventions when ingested multiple magnets. Endoscopic resection should be urgently performed in the presence of multiple magnets as early as possible within 24 hours, even in asymptomatic patients. Trial registration The study will be retrospectively registered.