A variable aperture model, instead of a conventional parallel plate model, is utilized to study the transport of radionuclides in a single coupled fracture-matrix system. A fully implicit finite difference model has been developed, which incorporates fracture aperture width variation in the numerical study of two species radionuclide transport. Two distinct geometric profiles namely, sinusoidal and logarithmic have been used to capture the variation of aperture width. The dependence of advection, hydrodynamic dispersion, linear sorption, and matrix diffusion on aperture width is considered in the analysis of radionuclides transport. Two species (parent and daughter) radioactive decay chain is also incorporated. There is a greater retardation of radionuclides in fracture for the variable aperture model than the parallel plate model. Sensitivity analysis on fracture surface sorption coefficient, longitudinal dispersivity, matrix porosity, and matrix diffusion coefficient shows that the conventional parallel plate model overestimate the radionuclide concentration in the fracture when compared to the variable aperture model. © 2016, The Association of Korean Geoscience Societies and Springer-Verlag Berlin Heidelberg.