We investigated the relationship between renal function assessment based on cystatin C (CsyC) and serum creatinine levels and the status of chemotherapy use in patients with gynecological cancer undergoing paclitaxel and carboplatin therapy. A significant positive correlation was found between estimated glomerular filtration rate from creatinine (eGFRcre) and eGFR from CsyC (eGFRcys) in the 98 patients included in the study. When eGFRcre and eGFRcys values were grouped according to GFR categories in the CKD severity classification, severe cases (eGFRcys < eGFRcre) were of more advanced age (P < 0.05) and had lower albumin levels (P < 0.01) than matched cases. Although no clear relationship was found between renal function assessment and chemotherapy status, the CysC and eGFRcys values tended to be higher and lower, respectively, in patients whose chemotherapy was deferred (P < 0.01 for CysC, P = 0.07 for eGFRcys). These results suggest that eGFRcre-based renal function assessment is overestimated compared with eGFRcys-based assessment in patients with gynecological cancer and may lead to carboplatin overdose or treatment deferral in elderly patients and patients with hypoalbuminemia.