We report the case of a patient with complement factor H gene variant, who developed thrombotic microangiopathy on a mixed clinical background. A 79-year-old woman was transferred to Sanjo General Hospital for maintenance hemodialysis. She suffered from gastric non-Hodgkin lymphoma about two years ago and received chemotherapy and radiation therapy, leading to complete remission. About 13 weeks prior to her transfer to our hospital, she was referred to another hospital due to acute kidney injury, hemolytic anemia, and thrombocytopenia. Hemodialysis was immediately initiated, after which intravenous methylprednisolone and oral prednisolone were started; however, she became anuric within approximately week. The possibility of thrombotic microangiopathy was examined. However, she was in poor general condition and did not get the consent of her family, so no invasive searches such as a kidney biopsy were performed. Despite the cause of acute kidney insufficiency being unclear, she was transferred to us for maintenance hemodialysis. Her general condition was stable, and her renal function improved; hence, two months after transfer, a kidney biopsy was performed. Her clinical and typical renal histological findings indicated a diagnosis of thrombotic microangiopathy. There was a possible CFH gene of a very rare variant "c.526 T > C (p.Phe176Leu)" in exon 5. She was able to withdraw from hemodialysis therapy two weeks after the initiation of an angiotensin-converting enzyme inhibitor. Based on her clinical course and kidney biopsy findings, she was diagnosed with thrombotic microangiopathy with a very rare CFH variant. To ensure proper treatment choices such as eculizumab, the presence of complement dysregulation should be considered in cases of secondary thrombotic microangiopathy.