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Background: Heparin-induced thrombocytopenia (HIT) is a potentially life-threatening complication of heparin anticoagulation. Recently, infection has been implicated in the development of HIT. Case presentation: We herein present a case of HIT diagnosed by a repeated functional assay. A 67-year-old female with diabetic nephropathy was admitted to our hospital with hypoxemia caused by volume overload. Due to her diuretic-resistant condition, dialysis therapy anticoagulated with low-molecular-weight heparin (LMWH) was initiated. The coagulation of the whole extracorporeal blood circuit occurred on day 13. Methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia derived from a catheter-related bloodstream infection (CRBSI) was detected on day 15. Based on the hypercoagulable state due to infection, we increased the heparin dose during dialysis therapy; however, coagulation of the dialysis circuit persisted. We suspected HIT on day 17 in spite of a normal platelet count and performed a functional assay, which was negative. Since thrombocytopenia subsequently developed, the functional assay was repeated and a positive result was obtained on day 27, which definitely established a diagnosis of HIT. Conclusions: Based on the present clinical course, MSSA bacteremia appears to have contributed to the pathogenesis of HIT.