Demonstration of all-solid state 3-dimensional (3D) Li-ion batteries has been a long standing goal for numerous researchers in the battery community interested in developing high power and high areal energy density storage solutions for variety of applications. The basic idea is to use the 3D geometry to maximize the volume of active material per unit area, while keeping its thickness sufficiently small to allow for fast Li diffusion. However, the introduction of 3D battery designs can result in a non-uniform electrolyte thickness in which the distance between the anode and cathode differs across different locations within the battery. This, in turn, can affect the battery performance. We explore, using finite element simulation methods, how a non-uniform electrolyte thickness can affect the ionic mass transport across a solid-state Li ion battery, and ultimately the performance of these types of batteries. We base our simulations on a working 3D solid-state (LiPON) Li ion battery, showing there is a good agreement between experiment and simulation. We explain how the performance of this battery is affected by the non-uniform thickness of the electrolyte, which introduces a non-uniform current density across both the anode/electrolyte and cathode/electrolyte boundaries.