A 34-year-old male presented with a rare case of Rathke's cleft cyst (RCC) with calcification manifesting as persistent high fever and impaired consciousness. Physical findings revealed panhypopituitarism and bitemporal hemianopsia. Computed tomography showed mass lesions with marked calcification within the sella turcica and the suprasellar region. Magnetic resonance imaging showed solid and cystic components compressing the optic nerve. The preoperative diagnosis was craniopharyngioma. Initial endonasal transsphenoidal surgery (TSS) was performed with a surgical microscope, but the mass was extremely hard, so only partial removal was possible. Second endonasal extended TSS was performed with a neuroendoscope. The solid components were totally removed, but calcifications adhering to the optic nerve could not be removed completely. The histological diagnosis was RCC with marked granulation reaction. RCC with calcification is rare and difficult to differentiate from craniopharyngioma on neuroimages. Extremely thick calcification of the sella turcica enclosing granulation tissue and the cyst similar to armor, here called "armor-like calcification," is a characteristic imaging finding of RCC with calcification. The most important aspect is choosing a surgical approach to carefully and effectively relieve pressure upon the optic nerve. Endonasal extended TSS with an endoscope was effective in the present case.