Background Rhinosporidiosis is a chronic infectious disease caused by an infection with the sporulating bacterium Rhinosporidium seeberi. It primarily affects the nose and nasopharynx mucous membranes, but it can also involve the conjunctiva. The most common presentation of ocular rhinosporidiosis is a polypoid mass in the palpebral conjunctiva. It affects people of all ages and genders and is found in few Asian countries. Conjunctival lesions are uncommon, and no previous case from Ethiopia has been documented to the authors’ knowledge. Case Presentation A 12-year-old boy with a fleshy pedunculated conjunctival mass was brought to Jimma University Medical Center with a 1-month history of foreign body sensation. The patient was diagnosed with Pedunculated Squamous Cell Papilloma and had an excisional biopsy of the lesion. The mass was found to be a hyperplastic polypoid lesion with numerous globular cysts within the conjunctival submucosa, surrounded by a heavy inflammatory infiltrate of lymphocytes, plasma cells, and neutrophils, as well as large thick-walled sporangia with numerous endospores on microscopic sections. Conjunctival Rhinosporidiosis was diagnosed histopathologically. Conclusion In terms of clinical appearance, conjunctival Rhinosporidiosis resembles squamous papilloma. As a result, a thorough histopathologic study is essential for a correct diagnosis of this uncommon condition.