Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage- and pH-dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function–structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions, and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins.