We report a case of subclinical central diabetes insipidus (DI), due to Rathke's cleft cysts, that was initially misdiagnosed as transient DI of pregnancy because it presented in the third trimester of pregnancy. A 37-year-old primigravida visited the Department of Obstetrics in the 30th week of gestation due to polyuria. She was admitted due to oligohydramnios; the amniotic fluid index was 3.24. A vasopressin challenge test was performed and her urine osmolality increased by >100% from baseline after the administration of desmopressin. Because central DI or transient DI of pregnancy was suspected, we prescribed her a desmopressin nasal spray. She gave birth to a relatively healthy baby at 37 weeks and 4 days of gestation. Several months after delivery, discontinuation of desmopressin resulted in recurrence of her polyuria. Magnetic resonance imaging of her brain revealed Rathke's cleft cysts, and finally central DI was diagnosed.