We report a rare case of congenital fibrosarcoma (CFS) showing regression during the course of disease, in which the histological and genetic alterations were investigated. This CFS, located on the patient's right hand, was a hemangiopericytomatous hypervascular tumor showing frequent mitosis and necrosis. Small lymphocytes, predominantly cytotoxic T cells and natural killer cells, infiltrated the tumor. At the age of 3 months, the patient received a partial resection of the tumor. At the age of 1 year, the hemangiopericytomatous tumor with a dilated vascular lumen remained, although most of the tumor cells exhibited focal necrosis with calcification and no mitotic activity. Lymphocytes increased in number and intermingled with the tumor cells. At the age of 4 years, vascular tissue consisting of inner endothelial cells and surrounding pericytomatous actin‐positive cells remained at the previous tumor locus. With reverse transcription–polymerase chain reaction analysis, ETV6–NTRK3 fusion transcripts were detected in tumor samples at 3 months and at 1 year, but not from those at 4 years of age. These genetic and histological changes suggest that the CFS either completely disappeared by apoptosis or showed mature transformation to hemangiomatous tissue with aging.