Background Pituitary stalk interruption syndrome (PSIS) is a rare congenital pituitary anatomical disorder. Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by congenital absence of the uterus, cervix, and part of the vagina in phenotypically normal 46, XX females. Case presentation A young woman was initially diagnosed as MRKH syndrome based on primary amenorrhea, 46, XX karyotype, and absence of uterus or vagina. Further investigation revealed breech delivery, short stature, hypogonadotropic hypogonadism, interrupted pituitary stalk on pituitary MRI, which led to the diagnosis of PSIS. After a 12-month treatment with estradiol, no signs of uterus or vagina were found on pelvic computed tomography.Conclusions We highlight the importance of considering PSIS in the differential diagnosis of suspected MRKH syndrome in prepubertal girls or girls with delayed or absent puberty, when no uterus is visualized on imaging.