Background: Malignant transformation of epidermal inclusion cysts (EICs) is rare. Only one case has been reported in the pericoccygeal-rectal region. Benign notochordal cell tumor (BNCT) is also rare. There have been no reports of squamous-cell carcinoma (SCC) arising in EICs with adjacent BNCT in the English-language literature. Case presentation: An 83-year-old male patient with a history of malignant fibrous histiocytoma of the thigh after resection and irradiation presented clinically with a pericoccygealrectal, flocculent, painful mass 7 cm in diameter. No osseous destruction was associated on magnetic resonance imaging. Partial sacrectomy and coccygectomy with en bloc resection of retrorectal cystic tumor were performed. Histology showed SCC arising from an EIC. SCC cells were positive for p53, EGFR, p16, and cytokeratin 5/6 on immunostaining and negative for human papillomavirus. Adjacent to the EIC, one tumor showed bland cells with numerous intracytoplasmic vacuoles. These cells were positive for epithelial membrane antigen, pancytokeratin, S100, and negative for CD68, which confirmed the diagnosis of BNCT. The diagnosis was well moderately differentiated invasive SCC arising in an EIC with an adjacent BNCT abutting to bone. Conclusion: We report the first case of SCC arising from an EIC with an adjacent BNCT in a patient with a history of malignant fibrous histiocytoma. Partial sacrectomy and coccygectomy with en bloc resection of retrorectal cystic tumor and wide margins taken prevented recurrence of both tumors.