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A cholesterol granuloma (CG) is characterized by the presence of cholesterol crystals that cause a chronic granulomatous reaction in an enclosed space. It occurs most commonly in the head and neck region, particularly in the middle ear. Although CGs in the maxilla have also been reported, odontogenic cysts in conjunction with CGs in the maxilla are very rare. We herein present a case of a 72-year-old man who developed a large primordial cyst with a maxillary CG that extended into the maxillary sinus, nasal cavity, and infraorbital region, causing left-sided facial swelling and discomfort. We successfully controlled the symptoms and reduced the size of the lesion using the treatment approach for a common odontogenic cyst: fenestration followed by complete excision. This case suggests that fenestration is an effective technique to treat odontogenic cysts with CGs. Although the mechanisms underlying the pathogenesis and growth of CGs are still unknown, our report highlights a potential therapeutic approach for these lesions.