We propose a method of non-invasively evaluating the permeability of cell membranes in normal rat brain using diffusion magnetic resonance imaging (MRI). Diffusion MRI signals reflect the intra- and extracellular diffusion coefficients of water molecules in permeable biological tissues and cell membranes. The signals were acquired using a 4.7 T MRI system and applying a motion-probing gradient (MPG) in six directions. Numerical simulations using the finite-difference method were conducted for various combinations of intracellular diffusion coefficients and cell-membrane permeabilities. We defined the evaluative function as the difference between the signals from numerical simulations and experimentally obtained signals. We found that the minimum value for the evaluative function enabled us to estimate the intracellular diffusion coefficient and membrane permeability of the rat brain, which were corresponded to (1.3±0.1) × 10-3 mm2/sec and 66±24 μm/sec. Our method was useful for non-invasively estimating the cell-membrane permeability of biological tissues, and can easily be applied to human tissues and other samples.