Purpose <p>Congenital malformations of the middle ear, particularly those affecting the ossicular chain and stapes, are uncommon yet significant causes of conductive hearing loss. Here, we report a unique case of stapes malformation with an empty oval window and provide a review of the literature to contextualize our findings.</p> Methods <p>We present the detailed diagnostic and therapeutic course of a 21-year-old female with unilateral conductive hearing loss, focusing on imaging, intraoperative findings, and management strategy. A comprehensive literature review (January 1950–January 2025) was undertaken in major databases.</p> Results <p>Preoperative high-resolution computed tomography (HRCT) revealed no apparent abnormalities. Exploratory tympanotomy, however, identified a malformed stapes located on the promontory, below an empty oval window covered by fibrous tissue. No bone was felt on palpation. In light of the risk for perilymphatic gusher and the moderate degree of hearing loss, surgical reconstruction was not performed. The patient was managed with hearing amplification, achieving satisfactory rehabilitation and no complications.</p> Conclusion <p>Malformations of the stapes and oval window demonstrate significant anatomical variability and can be difficult to diagnose using imaging alone. Surgical exploration remains crucial, and in the setting of an empty oval window, a tailored, conservative approach may be favored to minimize morbidity.</p>