Early studies show hysterectomy is a main surgical choice for cervical agenesis with excellent outcomes. However, as time went on more literature showed successful uterovaginal anastomosis performed in cervical agenesis. This case report wishes to highlight the management of the patient with complete vaginal and cervical agenesis, which presented with acute abdominal pain due to severe extension of the uterus. We aim to explore options and dilemmas in preserving reproductive function in such cases. A 13-year-old child was presented with acute abdominal pain and primary amenorrhea due to suspected vaginal agenesis. Physical examination revealed fundal height equal to 20 weeks of pregnancy. The vagina has no introitus and the external urethral meatus was normal. Abdominal ultrasound revealed a hematometra with the size of 8.84 × 3.12 cm accompanied by hematosalpinx on both fallopian tubes. The patient then undergoes an emergency hysterectomy. During the operation, it was found the cervix was substituted with the muscular part of the uterus with a little part of connective tissue part with no cardinal ligaments. Earlier articles showed hysterectomy is the first line of treatment in cervical agenesis. However, with the advancement of surgical techniques conservative treatment was made possible and reported in several case reports. According to European Society of Human Reproduction and Embryology (ESHRE) classification, our patient is classified as U0-C4-V4 (complete vaginal and cervix agenesis). We opted for a hysterectomy in this patient due possibility of fertility being slim and acute abdominal pain relief. Performing such a difficult operation in our setting requires expert meetings, and tool preparation also an amniotic graft for neovagina which in our case we could not afford due to the acute abdominal pain the patient experienced, and the patient's adamant wish for a hysterectomy. Hysterectomy remains a safer approach in low-resource settings with excellent postoperative outcomes. However, reconstructive surgery is an option that should be offered with its own risks and benefits.