We present a quantum chemical analysis of the structural and energetic characteristics of ion pairs that are most likely to be found in protic ionic liquids (PILs) — tripropylammonium bis(trifluoromethanesulfonyl)imide (TPrA/TFSI) and tripropylammonium hydrogen sulfate (TPrA/HSO4). To do the analysis, we determine the most active centers of the cation–anion interaction, model the structures of the possible ion pair configurations, and calculate the ion–ion interaction energies. Bader’s QTAIM analysis is used to evaluate the contributions of hydrogen bonds to the formation of the structure of the ion pairs of these PILs. We also report the results of experimental studies of the thermal stability, phase behavior, electrical conductivity, and dynamic viscosity of the synthesized TPrA/TFSI salt and compare them with those obtained previously for TPrA/HSO4. An analysis is done of the PIL structure effect on the obtained properties.