In this study, in-plane-oriented BaPrO3−δ thin film with mixed valence states has been prepared on an Al2O3(0001) substrate by RF magnetron sputtering. With increasing crystallization temperature (Tsub), the lattice constant decreases and the orientation changes from the a-axis to the b-axis. The thin film prepared above Tsub = 800 °C exhibits a higher proton conductivity than bulk ceramics. The conductivity below 400 °C decreases with oxygen gas partial pressure, indicating the existence of hole-ion mixed conduction. The valence band consists of O 2p states hybridized with the Pr4+ (4f0) and Pr3+ (4f1L) states, which are closely related to the mixed conduction. The energy difference between the top of the valence band and the Fermi level corresponds to the activation energy of holes for the total conductivity below 400 °C.