A 12-year-old child, previously raised as a female, presented with phallic enlargement at puberty. The sexual maturity ratings were Stage 2 and 4 for breast and pubic hair, respectively, with a stretched phallic length of 3.2cm. The patient re-presented at 16 years with progressive masculinisation and regression of breast buds. A pelvic ultrasound scan, magnetic resonant imaging and laparoscopic examination showed intrabdominal left testis, intracanalicular right testis, vas deferens, and bilateral pampiniform plexus with no uterus or ovaries. Histology of gonadal biopsy showed germ cell aplasia, and the karyotype was 46XY. The surgeons fixed the gonads in the scrotal sacs after biopsy. The human chorionic gonadotrophin stimulation test showed low basal and stimulated testosterone/androstenedione ratios (0.22 and 0.17, respectively) which were strongly suggestive of 17 beta-hydroxysteroid dehydrogenase-3 (17β-HSD3) deficiency. The patient was evaluated by the mental health team and after sessions of therapy, the patient requested for gender reassignment, which necessitated orthoplasty and urethroplasty. It is to be noted that 17β-HSD3 deficiency is a frequent cause of gender change at puberty.