Intraosseous lipoma is an uncommon mesenchymal tumor that is frequently found in appendecular skeleton. In extremely rare conditions, it can appear in sphenoid bone, and only 2 cases have been described in literature until now. We present a case of lipoma in the body of the sphenoid bone mimicking sphenoid sinus tumor. A 16-year-old man presented to Department of Otorhinolaryngology with a complaint of nonspecific headache. There were any clinical findings on physical examination. Computed tomography (CT) and magnetic resonance imaging (MRI) revealed and the diagnosis was made on these imaging findings. Other diagnostic technique, invasive histopathological assessment was not necessary. To our knowledge, this is the first case of lipoma in the body of the sphenoid bone with indentation to sphenoid sinus. The patient has been followed-up radiologically without the need for surgery for two years.