Earlier reports indicated that the conjugates (PEI(600)-CD, PC) of β-cyclodextrin and low-molecular-weight polyethylenimine (PEI, M(w) 600) can be used as efficient gene carriers in glioma cancer therapy. Incorporating anticancer drugs onto PC conjugates may endow them with new and interesting properties for great applications. In this work, FU-PEI(600)-CD (FPC) conjugates comprising PC and 5-fluoro-2'-deoxyuridine (FdUrd) were prepared as new bifunctional anticancer prodrugs with improved therapeutic effects, as well as good gene transfer efficiency. In comparison with free FdUrd, FPC could inhibit proliferation and enhance cytotoxicity on glioma cells. The results of hematoxylin and eosin (HE) staining indicated that C6 cells treated with FPC shrunk more seriously. Unlike FdUrd, cell cycle analysis indicated that C6 cells were primarily arrested in the G1 phase in the presence of FPC. Cellular uptake of FPC in C6 cells was about 10 times higher than that of FdUrd. In addition, the in vitro and in vivo gene transfection indicated that FPC still exhibited good gene expression efficiency. With the ability to deliver drugs and transfer genes, such bifunctional FPC conjugates may have great potential applications in combination therapy of cancers.