Primary amenorrhea is a symptom caused by different rare pathologic conditions. It is commonly seen during adolescence due to the absence of menses during this period. Presented here is a rare case of primary amenorrhea in an 18 year old girl with delayed pubertal growth and short stature which on series of investigations revealed hypergonadotropic hypogonadism, absence of the uterus and non-visualized bilateral ovaries on MRI. Karyotyping showed 45,X0. The coexistence of MRKH and gonadal dysgenesis was considered in this case and has been reported in only a few studies up to this date. Its association is uncommon, hence, a multidisciplinary approach is warranted for the management of her case. Further implications on menses and future fertility options are the main considerations, affecting the quality of life.