This work presents the investigation of functional properties of the yttrium-doped Ca3Co4O9+δ complex oxides as the prospective cathode materials for the proton-conducting fuel cells. The phase equilibria in the ½Y2O3–CaO–⅓Co3O4 system at 900 °C in air is experimentally observed, and the phase diagram is constructed. The misfit-layered structure of the Ca3-kYkCo4O9+δ solid solutions, and their chemical compatibility in air with proton-conducting electrolytes BaCe0.7 Ba3Ca1.18Nb1.82O8.73 are established. Functional properties of the obtained Ca3-kYkCo4O9+δ materials have been studied. The oxygen non-stoichiometry values of δ at room temperature are equal to 0.48 and 0.62 for Ca2.5Y0.5Co4O9+δ and Ca2YCo4O9+δ, respectively. The electrical conductivity in air reaches maximum value of 32 S cm−1 at 800 °C for Ca2.5Y0.5Co4O9+δ. The values of linear thermal expansion coefficient for Ca2.5Y0.5Co4O9+δ and Ca2YCo4O9+δ are equal to 13.5 × 10−6 and 14 × 10−6 K−1 in the temperature range of 25–800 °C in air. Minimum value of the polarization resistance Rp of 0.86 Ω cm2 at 600 °C is observed for the Ca2YCo4O9+δ electrode on the BaCe0.7Zr0.1Y0.1Yb0.1O3-δ substrate. Results of the work demonstrate that Y-doping of Ca3Co4O9+δ can be recommended as the successful strategy for the enhancement of the electrochemical performance of the cathodes, based on Ca3Co4O9+δ, in the solid oxide fuel cells with the proton-conducting electrolytes.