Over the last two decades, the focus of studies on graft survival (GS) after kidney transplantation (KT) has largely shifted from T-cell mediated rejection (TCMR) to antibody-mediated rejection (ABMR). However, there are still cases of pure acute TCMR in histological reports, even after a long time following transplant. We thus evaluated the impact of pure TCMR on GS according to treatment response. We also performed molecular diagnosis using a molecular microscope diagnostic system (MMDx) to determine the accuracy of the histologic diagnosis of pure TCMR. A total of 63 patients were included in our study and divided into non-responders (N = 22) and responders (N = 44) according to their response to rejection treatment. Molecular diagnosis and histologic diagnosis were conducted simultaneously on a separate group of 23 patients. The non-responders had a significantly longer duration between treatment and recurrent rejection than did the responders (24 vs. 11 months; P < 0.01). The cumulative incidence of recurrent rejection after treatment was significantly higher in the non-responders as well (64% vs. 29%; P < 0.01). Non-response to rejection treatment was significantly associated with the following factors: GFR at biopsy, ΔGFR (baseline GFR – GFR at biopsy), TCMR within one year, t score, and IF/TA score. We also found that non-responder vs. responder (HR = 3.31; P = 0.04) and lower GFR at biopsy per 10 mL/min/1.73m2 (HR = 0.56; P = 0.03) were independent risk factors of graft failure. The responders had a significantly superior overall GS rate compared with the non-responders (P < 0.01). Molecular assessment using MMDx showed a good correlation with histologic diagnosis in ABMR, but not in TCMR. Solitary TCMR was a significant risk factor of graft failure in patients who did not respond to rejection treatment. Molecular assessment using MMDx did not show a good correlation with histologic diagnosis in TCMR, suggesting that acute pure TCMR at one year after transplant in histologic reports should be interpreted with caution.