Extragastrointestinal tumour of rectovaginal septum (rvGIST) is a rare malignancy that affects rectovaginal septum. We present a case of rvGIST that was initially managed as cervical eGIST based on clinical assessment. A 66-year-old woman presented with postmenopausal bleeding and constipation. Bimanual pelvic examination revealed an irregular mass occupying the vagina. CT thorax, abdomen and pelvis showed a 9.2 x 10.0 x 14.0 cm pelvic mass arising from cervix, extending superiorly to involve the uterus. The patient proceeded to undergo total abdominal hysterectomy, bilateral salpingo-oophorectomy, enucleation of rectovaginal septum mass, rectosigmoidectomy and permanent colostomy. Intraoperatively, there was a 9 x 7 cm mass arising from rectovaginal septum. Histopathological examination of surgical specimen revealed spindle cell tumour diffusely positive for CD34, CD117 and DOG1. The final diagnosis was rvGIST. In conclusion, the diagnosis of rvGIST require a combination of clinical assessment with intraoperative finding and histological assessment of the surgical specimen.