The diffusion of radionuclides in cementitious materials used as an engineered barrier is an important parameter in the performance assessment of the sub-surface repository system used for low-level radioactive waste disposal in Japan. In particular, organic carbon-14 and iodine-129 would provide large contributions to the dose evaluation, because of their low ability to be adsorbed on cementitious materials. In this study, the diffusion of acetate and iodide in hardened cement pastes was examined by through-diffusion experiments. Low-heat Portland cement containing 30 wt% fly ash (FAC), which is a candidate cement material for the construction of the sub-surface repository, was prepared for the diffusion experiments. The effective diffusion coefficients, De, of the trace ions for hardened FAC cement pastes were estimated to be on the order of 10-13 m2 s-1 at the beginning of the diffusion experiments. Then, the rate of diffusion of the trace ions decreased over the experimental period of 1-15 months. This is probably due to the change in the microstructure of the FAC as the result of a pozzolanic reaction. After a few months, the values of De were estimated to be on the order of 10-14 m2 s-1. These results suggest that an engineered barrier made of FAC can act as an effective barrier inhibiting the diffusion of trace ions such as organic carbon and iodine.