The hexagonal perovskite Ba5In2Al2ZrO13 and In3+-doped phase Ba5In2.1Al2Zr0.9O12.95 were prepared by the solid-state synthesis method. The introduction of indium in the Zr-sublattice was accompanied by an increase in the unit cell parameters: a = 5.967 Å, c = 24.006 Å vs. a = 5.970 Å, c = 24.011 Å for doped phase (space group of P63/mmc). Both phases were capable of incorporating water from the gas phase. The ability of water incorporation was due to the presence of oxygen deficient blocks in the structure, and due to the introduction of oxygen vacancies during doping. According to thermogravimetric (TG) measurements the compositions of the hydrated samples corresponded to Ba5In2Al2ZrO12.7(OH)0.6 and Ba5In2.1Al2Zr0.9O12.54(OH)0.82. The presence of different types of OH−-groups in the structure, which participate in different hydrogen bonds, was confirmed by infrared (IR) investigations. The measurements of bulk conductivity by the impedance spectroscopy method showed that In3+-doping led to an increase in conductivity by 0.5 order of magnitude in wet air (pH2O = 1.92·10−2 atm); in this case, the activation energies decreased from 0.27 to 0.19 eV. The conductivity−pO2 measurements showed that both the phases were dominant proton conductors at T < 500 °C in wet conditions. The composition Ba5In2.1Al2Zr0.9O12.95 exhibited a proton conductivity ~10−4 S·cm−1 at 500 °C. The analysis of partial (O2−, H+, h•) conductivities of the investigated phases has been carried out. Both phases in dry air (pH2O = 3.5·10−5 atm) showed a mixed (oxygen-ion and hole) type of conductivity. The obtained results indicated that the investigated phases of Ba5In2Al2ZrO13 and Ba5In2.1Al2Zr0.9O12.95 might be promising proton-conducting oxides in the future applications in electrochemical devices, such as solid oxide fuel cells. Further modification of the composition and search for the optimal dopant concentrations can improve the H+-conductivity.