In this work, a three-dimensional microstructure-scale model of a Solid Oxide Fuel Cell’s Positive-Electrolyte-Negative assembly is applied for the purpose of investigating the impact of decreasing the electrolyte thickness on the magnitude, and the composition of electrochemical losses generated within the cell. Focused-Ion-Beam Scanning Electron Microscopy reconstructions are used to construct a computational domain, in which charge transport equations are solved. Butler−Volmer model is used to compute local reaction rates, and empirical relationships are used to obtain local conductivities. The results point towards three-dimensional nature of transport phenomena in thin electrolytes, and electrode-electrolyte interfaces.