Many biocolloids, biological cells and micro-organisms are soft particles, consisted with a rigid inner core covered by an ion-permeable porous membrane layer. The electrophoretic motion of a soft spherical nanoparticle in a nanopore filled with an electrolyte solution has been investigated using a continuum mathematical model. The model includes the Poisson–Nernst–Planck (PNP) equations for the ionic mass transport and the modified Stokes and Brinkman equations for the hydrodynamic fields outside and inside the porous membrane layer, respectively. The effects of the “softness” of the nanoparticle on its electrophoretic velocity along the axis of a nanopore are examined with changes in the ratio of the radius of the rigid core to the double layer thickness, the ratio of the thickness of the porous membrane layer to the radius of the rigid core, the friction coefficient of the porous membrane layer, the fixed charge inside the porous membrane layer of the particle and the ratio of the radius of the nanopore to that of the rigid core. The presence of the soft membrane layer significantly affects the particle electrophoretic mobility.