Background FK506-binding protein 12 (FKBP12) is abundant, ubiquitously expressed cytoplasmic protein with multiple functions in cell signaling transduction. Recently, we reported a novel function for FKBP12 in oncoprotein mouse double minute 2 (MDM2) self-ubiquitination and degradation, which greatly enhanced the sensitivity of cancer cells to chemotherapy. However, the clinical relevance remains unclear. Methods An immunohistochemical analysis of FKBP12 expression was performed in a cohort of 524 patients with invasive breast cancer. The correlations of FKBP12 expression with patient survival and chemoresponse were statistically analyzed. MDA-MB-468 cells were transfected with FKBP12 siRNA or Myc-tagged FKBP12, and then, the tumor cells were treated with doxorubicin followed by western blot, cell viability, and apoptosis assay. Results The expression of FKBP12 was decreased in breast cancer tissues, and there was a significant correlation between FKBP12 loss and MDM2 overexpression. Furthermore, FKBP12 loss was specifically correlated with poor prognosis and increased resistance to anthracycline-based chemotherapy. Kaplan-Meier survival analysis showed that overall survival (OS) and disease-free survival (DFS) were both significantly lower in the low FKBP12 expression group than those in the high FKBP12 expression group. In patients treated with anthracycline-based preoperative chemotherapy, low FKBP12 expression patients had a significant lower rate of pathologic complete response (pCR). Importantly, these results seemed to be driven mainly by MDM2. These observations were especially prominent in the MDM2-positive subgroup. Univariate and multivariate analyses revealed that FKBP12 loss was an independent factor for predicting prognosis and pCR. In in vitro assay, FKBP12 silence led to significant upregulation of MDM2. Accordingly, MDA-MB-468 cells with FKBP12 silence were less responsive to doxorubicin-induced cytotoxic and apoptotic effect. In contrast, in FKBP12-transfected MDA-MB-468 cells, MDM2 was more greatly inhibited by doxorubicin, resulting in greater cytotoxic and apoptotic effect. Conclusions We propose that FKBP12 loss, which can be enhanced by MDM2 overexpression, predicts poor prognosis and chemoresistance. Increasing the expression of FKBP12 may be a valuable strategy to add to anthracycline-based chemotherapy, especially in MDM2-overexpressed patients.