Protic ionic liquids (PILs) have been recently the subject of experiments for lithium-ion batteries (LIBs) applications, showing promising properties, in some cases better performance than aprotic ionic liquids (AILS). With the aim of a direct comparison between the performance of PIL and AIL electrolytes in LIBs, we conducted molecular dynamics simulations of corresponding lithium-salt-doped electrolytes. Our PIL and AIL electrolytes are triethylammonium bis(trifluoromethanesulfonyl)imide ([N222][TFSI]) and triethylmethylammonium bis(trifluoromethanesulfonyl)imide ([N1222][TFSI]), respectively, each doped with LiTFSI. Three fundamental structural changes were observed upon the addition of Li salt into IL solutions: (1) formation of rigid Li-TFSI complexes, (2) cation-anion coordination became larger, and (3) formation of Li aggregates. Moreover, we observed that the density and viscosity of the electrolytes increased with increasing lithium salt mole fraction (x(Li)), and correspondingly, the self-diffusivity of ions, ionic conductivity, and ionicity became lower. The Li conductivity exhibits a maximum at x(Li) = 0.2 due to the competition between increasing Li salt concentration and viscosity. More importantly, the PIL electrolytes display higher Li conductivity and better transport properties over their AIL counterpart.