Pure primary ovarian squamous cell carcinoma (SCC) is a rare histological type with a poor prognosis. Herein, we present the first reported case of advanced pure primary ovarian SCC with homologous recombination deficiency (HRD). A 65-year-old woman who underwent emergency surgery because of acute abdominal pain was diagnosed with SCC of the ovary and was referred to our department for further treatment. Thorough investigations revealed no signs of other primary sites of SCC except for the left ovary. Postoperative positron emission tomography-computed tomography showed residual tumor. Since pure primary ovarian SCC typically shows a poor response to chemotherapy, we decided to perform debulking surgery. Total abdominal hysterectomy, right salpingo-oophorectomy, pelvic lymphadenectomy, para-aortic lymphadenectomy, bowel resection and left partial ureterectomy were performed. Postoperatively, there was no residual tumor larger than 1 cm. Postoperatively, she developed pelvic infection that prolonged her hospital stay due to the need for antibiotics. However, there were no other perioperative complications and she was discharged. SCC with keratinization was observed on histopathological examination of metastatic lymph nodes. An HRD companion diagnostic test performed on the resected specimen was positive for HRD (score 57) and negative for BRCA 1/2 mutations. She received six courses of paclitaxel and carboplatin followed by maintenance therapy with niraparib, which is continuing. There are no signs of recurrence as of the one-year follow-up after surgery. We presented a rare case of advanced pure primary ovarian SCC with HRD. Complete surgical removal of HRD-positive pure primary ovarian SCC may lead to long-term survival with subsequent chemotherapy followed by maintenance therapy with poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors.