Trade-off parameters (proton conductivity and chemical stability) among standalone and acceptor-doped proton-conducting electrolytes hinder their practical utility within the fuel cell technology. The physio and electrochemical divergence among the proton conducting electrolytes introduce thermionic singularity (fluctuation) due to multifacet contributions ranging from structural phase transitions to defect-cluster distribution. Meanwhile, lattice disorder (phonon contributions) and defect scattering events distort the charge transport characteristics of the host material. As a result, in the present study we address the thermionic response of standalone and Y3+ doped BaCeO3 polymorph using first principles and classical molecular dynamics to contemplate proton landscape and dynamical disorder among aristotype and hettotype structures. The outcome of the study illustrates a promising thermionic behaviour among hettotype structures due to desirable potential energy surface with finite tunnelling probability relative to aristotype counterpart. As a result, a favourable response by BaCe0.75Y0.25O3-δ (rhombohedral symmetry) at intermediate temperature (400–580 °C) occurs due to phonon aided proton transport, desirable proton landscape (O–O separation), weaker Y–O hybridization and high carrier concentration. However, thermionic fluctuations and contrary response at elevated temperatures (>600 °C) illustrate the advent of ambipolar characteristics (H+/O2−), cationic disorder (Ce4+ → Ce3+), defect scattering (VO..) event and local proton traps due to proton-polaron charge redistribution. As a result, the present study is essential to enhance the electrochemical kinetics and performance efficiency of proton conducting electrolytes.