The membrane transport properties of 5-FU and its prodrugs were investigated using Caco-2 cell monolayers. To elucidate a membrane transport of prodrug itself, 2-O-alkoxy-5-fluoropyrimidone (2-O-alkoxy-5FP) derivative, which was stable in buffer and Caco-2 cell, was selected as a test compound. The permeation of 2-O-alkoxy-5FP derivatives was markedly greater than that of 5-FU. The dose-dependency of apical to basal (AP-BL) and BL-AP transports showed that 5-FU was dominantly transported by passive diffusion and ethoxy-5FP was transported by passive diffusion and unsaturated efflux transporter in the apical membrane of Caco-2 cell monolayers. Furthermore, treatment of Cap-Na, an enhancer of paracellular transport, demonstrated that 5-FU and 2-O-alkoxy-5FP derivatives permeated through paracellular and transcellular route, respectively. The significantly increased permeability of 2-O-alkoxy-5FP derivatives was mainly related to capping of hydrophilic functional group, and the moderate increase in permeability among 2-O-alkoxy-5FP derivatives was dependent on prolongation of the alkyl chain length.