Rectal mucosal prolapse is uncommon in children. While most patients present with rectal bleeding and constipation, the occurrence of osseous metaplasia within the prolapsed mucosa is extremely rare. Overlapping clinical, gross, and histological features between rectal mucosal prolapse polyps and malignancy pose a challenge for diagnoses. We describe a case of a 16-year-old male who had a rectal mucosal prolapsed polyp with osseous metaplasia. He initially presented due to periumbilical pain with a sore throat and fever. Incidentally, during the workup of his periumbilical pain, he was found to have a soft tissue mass in his rectum on a CT scan, with a biopsy confirming the diagnosis. The case was complicated by the development of sepsis. The patient was treated with empiric antibiotics and was discharged without further complications.