Double-layered perovskite oxides of Pr1−yBaCo2O5+δ (P1−yBCO) with A-site Pr3+-deficiency contents of y = 0.00–0.10 have been studied with respect to phase structures, oxygen content, high-temperature chemical stabilities as well as electrical and electrochemical properties as cathode materials of intermediate-temperature solid oxide fuel cells (IT-SOFCs). The Pr3+-deficiency content in P1−yBCO is limited by ∼8 mol%, and the Pr3+-deficiency hardly changes lattice parameters of P1−yBCO. Content of oxygen vacancies increases while that of Co4+ decreases with the higher Pr3+-deficiency content. P1−yBCO is chemically stable with the Gd0.1Ce0.9O1.95 (GDC) electrolyte at 1100 °C and below in air. Introduction of Pr3+-deficiency decreases electrical conductivities and significantly improves electrochemical performance of P1−yBCO. Among the studied oxides, P0.95BCO with 5 mol% Pr3+-deficiency shows the best electrochemical performance with low ASR values of 0.113 Ω cm2 at 600 °C, 0.054 Ω cm2 at 650 °C and 0.028 Ω cm2 at 700 °C respectively, demonstrating it a promising cathode material of IT-SOFCs. The results of P1−yBCO have also been compared with those of Ba2+-deficient PrBa1−xCo2O5+δ (PB1−xCO, x = 0.00–0.10) oxides and major differences have been found in lattice parameters, oxygen content, chemical defects, electrical conductivities and ASR results. Factors contributing to these differences have been discussed.