A cadmium-responsive metal ion transporter OsPDR, which was highly upregulated in the shoot of rice (Oryza sativa ssp. japonica cv. Nipponbare) at 24 h after treatment with 50 μmol/L Cd, was identified in cadmium-responsive transcriptome profiles analyzed by RNA-Seq. In this study, we isolated OsPDR from rice (Oryza sativa cv. Nipponbare) and the metal ions transport activity of OsPDR was analyzed. The results of metal tolerance experiments showed that overexpression of OsPDR can enhance yeast’s tolerance to Co, but not to Zn, Ni or Cd, and higher accumulation of Co was observed compared to the empty vector-transformed yeast as determined by inductively coupled plasma mass spectrometry (ICP-MS). The EGFP-OsPDR fusion protein was localized to the vacuolar membrane using confocal microscopy. These data suggested that OsPDR might play an important role in Co homeostasis. Additional studies are needed to understand the function of OsPDR in plants.