Background Yolk sac tumor (YST) is a germ cell tumor that is generally associated with good prognosis in children. It has been recently reported that vaginal YSTs can be cured using chemotherapy alone. Thus, minimal invasiveness and function preservation are pre-requisites for surgical approaches. Herein, we report a case of vaginal YST that was resected in a function-preserving manner using a unique combination of surgical approaches. Case presentation In a 9-month-old Asian female infant, a vaginal tumor was detected while investigating for vaginal bleeding. The patient was referred to our hospital, and the tumor was diagnosed as a YST after incisional biopsy. Six courses of carboplatin-based chemotherapy were administered. Contrary to the findings in previous reports, the tumor was chemo-resistant and surgical resection was required for the residual tumor. During surgery, we utilized laparoscopic and endoscopic procedures to ensure tumor-free surgical margins at the cervix, rectum, and lateral wall of the vagina. Additionally, the posterior sagittal approach was used to easily resect the tumor, and the vagina was reconstructed leaving only inconspicuous scars in the intergluteal cleft. No complications occurred postoperatively. Pathological examination of the surgical specimen revealed tumor-free surgical margins. The patient received four cycles of intensified chemotherapy before and after the surgery. The patient has been disease-free for 6 months now. Conclusions Our combination of laparo/endoscopic and posterior sagittal approach ensured a tumor-free macroscopic surgical margin with easier, cosmetically pleasing vaginal reconstruction, while preserving the anorectal and urinary functions. We believe that this approach could be utilized not only for vaginal YST, but also for any vaginal tumor, especially those arising from the posterior or lateral wall.