Mechanical modeling of the deformation of a liquid-filled spherical microcapsule indented by a sharp truncated-cone indenter was proposed, in which membrane permeability was taken into account. The change in the internal volume of the microcapsule due to fluid permeation was calculated on the basis of Kedem and Katchalsky equations (1958, “Thermodynamic Analysis of the Permeability of Biological Membranes to Non-electrolytes,” Biochim. Biophys. Acta, 27, pp. 229–246). The membrane hydraulic permeability, membrane initial stretch, and effective osmotic pressure difference across the membrane of an alginate–poly(l)lysine–alginate (APA) microcapsule were identified by fitting calculated and measured force–displacement curves. The difference between deformed shapes with and without membrane permeability was shown, suggesting the spatial resolution of image analysis performed to measure the membrane permeability from the volume loss. The influences of changes in permeability, initial stretch, and a parameter , used for determining the effective osmotic pressure difference, on the force–displacement relationship were examined, and mechanisms causing changes in the force–displacement relationship were discussed.