Idiopathic granulomatous hypophysitis (GH) is a rare inflammatory disease of the pituitary gland. A 48-year-old woman was admitted to the hospital with an irregular menstrual cycle. MRI showed pituitary cystic lesion with sellar enlargement. The patient underwent endoscopic endonasal transsphenoidal surgical excision. A histopathological assessment revealed non-necrotizing granulomatous lesions and a diagnosis of GH was made. The rarity of GH and cystic form of the disease make it difficult to confirm the diagnosis until surgery. We herein report this rare case and provide a discussion of the MRI findings and relevant literature of GH.