This work reports a comprehensive theoretical study of the transport-rectification properties of cylindrical nanopores with neutral inner walls and chemically modified outer membrane. The chemical species on the two outer sides of the membrane have charges of opposite sign and can be either surface-confined species (i.e., surface charges) or polyelectrolyte brushes. The advantage of this design over other types of rectifying nanopores is that it requires controlling the composition of the outer walls of the pore (which are easy to access) rather than the inner walls, thus simplifying the fabrication process. Ion-current rectification in nanopores with charged outer walls is ascribed to applied-potential-induced changes in the ionic concentration within the pore. The rectification efficiency is studied as a function of pore length, radius, surface charge and bulk electrolyte concentration. An analytical model is derived for the case of surface-confined charges that predicts the current–potential curves in very good agreement with the numerical calculations. Neutral nanopores with polyelectrolyte-modified outer walls have two distinct advantages compared to surface-charged systems: (i) they exhibit higher rectification factors due to the large charge density immobilized by the polyelectrolyte brushes, and (ii) the applied potential deforms the polyelectrolyte chains toward the oppositely charged electrode. This deformation brings the polyelectrolyte brushes into the pore in the low conductivity state and expels them from the pore in the high conductivity regime. Calculations of the potentials of mean-force suggest that the applied-field-induced conformational changes can be used to control the translocation of cargoes larger than ions, such as proteins and nanoparticles.