Transverse vaginal septum is a rare anomaly that results from incomplete fusion of urogenital sinus, and the vaginal parts of the Mullerian duct. Cervical atresia/dysgenesis is still a rare uterovaginal anomaly that can be congenital or acquired leading to fertility problems. Transverse vaginal septum when it coexists with cervical dysgenesis, it becomes a rare combination where management becomes highly complex. This case report deals with interdisciplinary role of conservative surgical management and custom made prosthetic appliances in the management of transverse vaginal septum and cervical atresia at an early stage and perhaps this goes to be the first-line treatment option with the expertise in laparoscopic surgery along with prosthetic management.