Comparisons between a LiPF6·PEO20 polymer electrolyte and a 1.5M LiPF6 liquid electrolyte in a 3D-microbattery of coated interdigitated current collector pillars is presented here, using Finite Element Analysis (FEA). Ionic transport in the electrolyte is modeled by the Nernst–Planck equation and electrode potentials by Ohm's law. Simulations were carried out in steady state. The height of the electrode pillars and the distance between them were systematically varied in the simulations to evaluate the effects on ionic transport in terms of concentration, concentration gradient and the minimum concentration in the electrolyte. The studies showed that the polarization in the electrolyte can be decreased by increasing the electrode pillar length, while increasing electrode distances led to a nonuniformity of the electrochemical activity. Indications of an optimum pillar length were also observed. Comparisons of the electrolytes showed that the polymer electrolyte was able to deliver a more uniform electrochemical activity for these cell designs, but not able to sustain as high currents as the liquid electrolytes. At the current density used (10A/m2), concentration polarization in the polymer electrolyte led to concentration deviations from the mean value of up to 60%.