Barium zirconate doped with 20 mol% Yb (BaZr0.8Yb0.2O3-δ, BZYb20) is one of the most promising candidates for use as an electrolyte material in protonic ceramic fuel cells (PCFCs) due to its high proton conductivity and high chemical stability under CO2-containing fuel conditions. The long-term durabilities of PCFCs prepared using the BZYb20 electrolyte were evaluated as a function of the current density at 500 and 600 °C over a period of 1000 h. At 600 °C, the internal resistance of the cell increased even under open circuit voltage (OCV) condition. Comparing the voltage lowering rates at a current density of 0.172 A cm−2 based on the current density–voltage curves recorded during the durability tests, rates of 3.0, 5.3, and 9.0%/1000 h were achieved at the OCV, 0.047, and 0.172 A cm−2, respectively. A small amount of Ni elements diffused into the electrolyte from the anode to the cathode side, resulting in the formation of cumulus cloud shapes that corresponded to Ni element segregation at the grain boundaries in the electrolyte layer after long-term durability testing at 0.172 A cm−2. At current densities of 0.047–0.048 A cm−2, the voltage lowering rate at 500 °C was higher than that at 600 °C, with values of 6.0 and 2.6%/1000 h being recorded, respectively. This effect may be due to the higher resistance of the cell at 500 °C compared to that at 600 °C.