Abstract Objective . The complex-valued transverse magnetization due to diffusion-encoding magnetic field gradients acting on a permeable medium can be modeled by the Bloch–Torrey partial differential equation. The diffusion magnetic resonance imaging (MRI) signal has a representation in the basis of the Laplace eigenfunctions of the medium. However, in order to estimate the permeability coefficient from diffusion MRI data, it is desirable that the forward solution can be calculated efficiently for many values of permeability. Approach . In this paper we propose a new formulation of the permeable diffusion MRI signal representation in the basis of the Laplace eigenfunctions of the same medium where the interfaces are made impermeable. Main results. We proved the theoretical equivalence between our new formulation and the original formulation in the case that the full eigendecomposition is used. We validated our method numerically and showed promising numerical results when a partial eigendecomposition is used. Two diffusion MRI sequences were used to illustrate the numerical validity of our new method. Significance. Our approach means that the same basis (the impermeable set) can be used for all permeability values, which reduces the computational time significantly, enabling the study of the effects of the permeability coefficient on the diffusion MRI signal in the future.