The perovskite-related oxides with intergrowth structure are a novel and promising class of protonic conductors. The development of this class of materials makes it possible to develop proton-conducting ceramics for intermediate temperatures (300–600 °C) for SOFCs (solid oxide fuel cells) applications. In this work, new complex oxide Ba5Y0.5In1.5Al2ZrO13 was obtained and investigated as a protonic conductor. Ba5Y0.5In1.5Al2ZrO13 shows the ability to water uptake and exhibits higher values of hydration degree (~ 0.40 mol H2O) than parent compound Ba5In2Al2ZrO13 (~ 0.30 mol H2O). IR spectroscopy confirmed the presence of OH−-groups in the hydrated phase Ba5Y0.5In1.5Al2ZrO13. The hydration ability is explained by the possibility of increasing the coordination number of barium in oxygen-deficient layers and the presence of sufficient space for the participation of OH−-groups in its coordination. Investigation of transport properties shows that in wet air (pH2O = 1.92·10−2 atm) below ~ 700 °C the conductivity is predominantly protonic. Proton mobility calculations show that the introduction of yttrium into the indium sublattice leads to an increase in mobility, which is probably due to an increase in the unit cell volume.