Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome is a rare congenital disorder characterized by the absence or underdevelopment of the uterus and upper part of the vagina in females with a normal 46, XX karyotype. It affects approximately 1 in 4500–5000 female live births and ranks as the second-most common cause of primary amenorrhea. This case report describes a 28-year-old nulligravid woman who presented with primary amenorrhea, difficulties during sexual intercourse manifesting as pain and resistance, and an incidental finding of a right ovarian new growth. Physical examination revealed normal secondary sexual characteristics and a blind-ending vagina measuring 5 cm in depth. Transvaginal ultrasound confirmed the presence of a transverse vaginal septum with hematocolpos, an infantile uterus with endometrium and cervix, a right ovarian new growth, and a normal left ovary. Both kidneys appeared normal, and hormonal assays were within normal limits. Karyotype analysis confirmed a genotype of 46, XX, indicating a normal chromosomal complement for a female without any detectable structural or numerical chromosomal abnormalities, consistent with typical female development. She subsequently underwent ultrasound-guided excision of the transverse vaginal septum combined with laparoscopic oophorocystectomy. Intraoperatively, findings included a normal left ovary, a right ovarian new growth, absence of fallopian tubes, and an infantile uterus. Histological analysis confirmed a serous cystadenoma in the right ovary. Karyotype analysis confirmed a genotype of 46, XX. The index case was diagnosed with MRKH type II (atypical), characterized by the absence of fallopian tubes and a right ovarian new growth without associated renal, skeletal, or cardiac anomalies.