Vaginal agenesis combined with a functional uterus is a rare condition in which treatment modalities that preserve reproductive function are controversial. A 21 year old female presented with congenital vaginal agenesis combined with cervical atresia. She was treated with gonadotrophin-releasing hormone (GnRH) agonists for a total period of over 5 years when a non-functioning pituitary tumour was detected by brain magnetic resonance imaging (MRI). A laparoscopically assisted reconstruction of a neovagina and neoendocervical canal was performed utilizing lyophilized porcine dermal skin to line the neovagina. Endometriosis of the pelvis was revealed and adhesiolysis and cauterization were also carried out under laparoscopy. The GnRH agonist was discontinued and the patient resumed cyclic menses with no abdominal pain. The pituitary tumour decreased in size 6 months after the cessation of GnRH agonists. We raise the question as to whether pituitary MRI should be performed for patients who need long-term administration of GnRH agonists.