Germ cell tumors are a group of malignant neoplasms originating from the primary germ cells of the human embryo. The incidence of the vaginal yolk sac tumors is 3—5%. In early childhood the formation has a number of special features. An increased level of alpha-fetoprotein in the manifest period of the disease can be interpreted as an age norm that complicates timely diagnosis. When performing surgery with classical vaginal access in newborns a small amount of tissues remaining for subsequent reconstruction inevitably makes the operation crippling. This case report demonstrates patient I., 4 months old, who was admitted urgently to Morozov´s Hospital in December 2023. According to mother´s words the child had spontaneous bloody discharge from the genital tract. Based on the data of laboratory and instrumental methods as well as histology a child was diagnosed with “vaginal yolk sac tumor”. Due to the rapid growth of the formation according to MRI-imaging as well as serum alpha-fetoprotein steadily increasing a chemotherapy was conducted. After two courses a significant regression of the size was registered, however, surgical treatment was prescribed by the consultation due to the resistance of the remaining part of the tumor to the drugs. This case report demonstrates the possibility of minimally invasive surgical intervention on the vagina of a newborn by vaginoscopy that shows compliance with the basic principles of oncosurgery along with the possibility of reproductive and sexual functions preservation in the future.