Introduction Hairy polyps are rare congenital choristomas of ectodermal and mesodermal origin. Fewer than twenty cases of Eustachian-tube (ET) origin have been reported, and bidirectional extension into both the middle ear and nasopharynx has not previously been described. Case Report A two-year-old female presented with persistent right otorrhoea from infancy, with canal granulation raising concern for congenital cholesteatoma. MRI demonstrated a 56 × 26 × 19 mm fat-containing Y-shaped lesion arising from the ET, extending both into the middle ear and nasopharynx with erosion of the osseous tubal segment. Pre-operative planning incorporated Stealth CT navigation and patient-specific 3D-printed models to define surgical approach and tumour trajectory. The lesion was excised via a combined post-auricular, transcervical, transoral and endonasal approach with continuous facial nerve monitoring, canal-wall-down mastoidectomy and blind-sac closure. Histopathology confirmed a hairy polyp composed of keratinising squamous epithelium, adipose tissue and muscle without endodermal elements or malignancy. Results: Complete excision was achieved without neurovascular injury or postoperative complications. Otorrhoea resolved and the patient remains recurrence-free with normal facial nerve function at follow-up. Discussion: This represents the first documented ET hairy polyp with true bidirectional extension into the middle ear and nasopharynx. It is also the first reported use of navigation and patient-specific 3D modelling to guide surgical planning in this pathology. The case highlights diagnostic difficulty, as ET lesions may mimic chronic otitis media or cholesteatoma and demonstrates the value of a multidisciplinary approach for safe resection. Conclusion: ET hairy polyps are exceedingly rare and may present atypically. Integration of navigation and 3D modelling provides a reproducible framework for managing complex congenital lesions involving skull-base compartments.