The reliability of solid oxide fuel cells (SOFCs) particularly depends on the high quality of solid oxide electrolytes. The application of thinner electrolytes and multi electrolyte layers requires a more reliable characterization method. Most of the investigations on thin film solid electrolytes have been made for the parallel transport along the interface, which is not however directly related to the fuel cell performance of those electrolytes. In this work an array of ion-blocking metallic Ti/Au microelectrodes with about a $160{mu}m$ diameter was applied on top of an ultrathin ($1{mu}m$) yttria-stabilized-zirconia/gadolinium-doped-ceria (YSZ/GDC) heterolayer solid electrolyte in a micro-SOFC prepared by PLD as well as an 8-${mu}m$ thick YSZ layer by screen printing, to study the transport characteristics in the perpendicular direction relevant for fuel cell operation. While the capacitance variation in the electrode area supported the working principle of the measurement technique, other local variations could be related to the quality of the electrolyte layers and deposited electrode points. While the small electrode size and low temperature measurements increaseed the electrolyte resistances enough for the reliable estimation, the impedance spectra appeared to consist of only a large electrode polarization. Modulus representation distinguished two high frequency responses with resistance magnitude differing by orders of magnitude, which can be ascribed to the gadolinium-doped ceria buffer electrolyte layer with a 200 nm thickness and yttria-stabilized zirconia layer of about $1{mu}m$. The major impedance response was attributed to the resistance due to electron hole conduction in GDC due to the ion-blocking top electrodes with activation energy of 0.7 eV. The respective conductivity values were obtained by model analysis using empirical Havriliak-Negami elements and by temperature adjustments with respect to the conductivity of the YSZ layers.