Abstract Introduction Choanal polyps are benign lesions arising from the sinonasal mucosa, extending through the choana into the nasopharynx. Though polyps arising from the maxillary sinus and extending to the choana are common, polyps arising from the sphenoid sinus ostium, posterior part of middle turbinate, and inferior and middle meatus are quite uncommon. Objective To document the site of origin of choanal polyps arising from unusual sites; their clinical, radiological, and histopathological characteristics, as well as diagnostic challenges and management. Methods This retrospective, single-center study included 14 patients aged 16 to 75-years-old with choanal polyps. After obtaining informed consent, their clinical, radiological and surgical details and histopathology reports were reviewed. Patients were followed for at least 6 months after surgery. Results The predominant symptoms were unilateral nasal obstruction (n = 9), snoring, rhinorrhea, and epistaxis. Though anterior rhinoscopy was unremarkable, a mass could be visualized during posterior rhinoscopy in the nasopharynx in 11 patients, and a mass could be directly visualized in the oropharynx in 2 patients. After diagnostic by nasal endoscopy, these polyps were noted to arise from the posterior aspect of the middle meatus (n = 6), middle turbinate (n = 3), posterior septum (n = 3), sphenoid sinus ostium (n = 1), and inferior meatus (n = 1). All patients were managed surgically. The histopathological examination revealed inflammatory polyp (n = 12), actinomycosis (n = 1), and rhinosporidiosis (n = 1). Patients were followed up for 6 to 22 months. We observed no complications or recurrence. Conclusion Diagnostic nasal endoscopy should be performed in all patients presenting with nasal obstruction, to rule out choanal polyps arising from unusual sites. Complete polyp removal and appropriate treatment based on histopathology prevents recurrence.